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List of Contributors | |
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Preface | |
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Acknowledgments | |
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Introduction and Text Overview | |
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The Elements of Life | |
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Functional Roles of Biological Inorganic Elements | |
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A Guide to This Text | |
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Overviews of Biological Inorganic Chemistry | |
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Bioinorganic Chemistry and the Biogeochemical Cycles | |
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Introduction | |
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The Origin and Abundance of the Chemical Elements | |
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The Carbon/Oxygen/Hydrogen Cycles | |
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The Nitrogen Cycle | |
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The Sulfur Cycle | |
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The Interaction and Integration of the Cycles | |
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Conclusions | |
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Metal Ions and Proteins: Binding, Stability, and Folding | |
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Introduction | |
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The Metal Cofactor | |
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Protein Residues as Ligands for Metal Ions | |
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Genome Browsing | |
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Folding and Stability of Metalloproteins | |
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Kinetic Control of Metal Ion Delivery | |
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Special Cofactors and Metal Clusters | |
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Why Special Metal Cofactors? | |
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Types of Cofactors, Structural Features, and Occurrence | |
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Cofactor Biosynthesis | |
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Transport and Storage of Metal Ions in Biology | |
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Introduction | |
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Metal Ion Bioavailability | |
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General Properties of Transport Systems | |
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Iron Illustrates the Problems of Metal Ion Transport | |
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Transport of Metal Ions Other Than Iron | |
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Mechanisms of Metal Ion Storage and Resistance | |
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Intracellular Metal Ion Transport and Trafficking | |
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Summary | |
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Biominerals and Biomineralization | |
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Introduction | |
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Biominerals: Types and Functions | |
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General Principles of Biomineralization | |
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Conclusions | |
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Metals in Medicine | |
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Introduction | |
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Metallotherapeutics | |
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Imaging and Diagnosis | |
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Molecular Targets | |
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Metal Metabolism as a Therapeutic Target | |
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Conclusions | |
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Metal Ion Containing Biological Systems | |
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Metal Ion Transport and Storage | |
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Transferrin | |
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Introduction: Iron Metabolism and the Aqueous Chemistry of Iron | |
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Transferrin: The Iron Transporting Protein of Complex Organisms | |
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Iron-Donating Function of Transferrin | |
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Interaction of Transferrin with HFE | |
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Ferritin | |
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Introduction: The Need for Ferritins | |
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Ferritin: Nature's Nanoreactor for Iron and Oxygen | |
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Siderophores | |
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Introduction: The Need for Siderophores | |
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Siderophore Structures | |
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Thermodynamics of Ferric Ion Coordination by Siderophores | |
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Outer-Membrane Receptor Proteins for Ferric Siderophores | |
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Marine Siderophores | |
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Metallothioneins | |
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Introduction | |
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Classes of Metallothioneins | |
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Induction and Isolation | |
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Structural and Spectroscopic Properties | |
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Reactivity and Function | |
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Copper-Transporting ATPases | |
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Introduction: Wilson and Menkes Diseases | |
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Structure and Function | |
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Metal Ion Binding and Conformational Changes | |
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Metallochaperones | |
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Introduction | |
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The Need for Metallochaperones | |
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COX17 | |
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ATX1 | |
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Copper Chaperone for SOD1 | |
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Metallochaperones for Other Metals? | |
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Concluding Remarks | |
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Hydrolytic Chemistry | |
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Metal-Dependent Lyase and Hydrolase Enzymes. (I) General Metabolism | |
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Introduction | |
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Magnesium | |
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Zinc | |
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Manganese | |
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Metal-Dependent Lyase and Hydrolase Enzymes. (II) Nucleic Acid Biochemistry | |
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Introduction | |
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Magnesium-Dependent Enzymes | |
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Calcium | |
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Zinc | |
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Urease | |
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Introduction | |
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The Structure of Native Urease | |
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The Structure of Urease Complexed with Transition State and Substrate Analogues | |
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The Structure-Based Mechanism | |
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The Structure of Urease Complexed with Competitive Inhibitors | |
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The Molecular Basis for in vivo Urease Activation and Nickel Trafficking | |
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Aconitase | |
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Introduction | |
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Stereochemistry of the Citrate-Isocitrate Isomerase Reaction | |
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Characterization and Function of the Fe-S Cluster | |
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Active Site Amino Acid Residues and the Reaction Mechanism | |
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Cluster Reactivity and Cellular Function | |
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Catalytic Nucleic Acids | |
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Introduction and Discovery of Catalytic Nucleic Acids | |
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Scope and Efficiency of Catalytic Nucleic Acids | |
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Classification of Catalytic Nucleic Acids with Hydrolytic Activity | |
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Metal Ions as Important Cofactors in Catalytic Nucleic Acids | |
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Interactions between Metal Ions and Catalytic Nucleic Acids | |
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The Role of Metal Ions in Catalytic Nucleic Acids | |
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Expanding the Repertoire of Catalytic Nucleic Acids with Transition Metal Ions | |
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Application of Catalytic Nucleic Acids | |
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From Metalloproteins to Metallocatalytic Nucleic Acids | |
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Electron Transfer, Respiration, and Photosynthesis | |
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Electron-Transfer Proteins | |
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Introduction | |
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Determinants of Reduction Potentials | |
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Iron-Sulfur Proteins | |
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Cytochromes | |
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Copper Proteins | |
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A Further Comment on the Size of the Cofactor | |
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Donor-Acceptor Interactions | |
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Electron Transfer through Proteins | |
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Introduction | |
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Basic Concepts | |
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Semiclassical Theory of Electron Transfer | |
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Photosynthesis and Respiration | |
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Introduction | |
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Qualitative Aspects of Mitchell's Chemiosmotic Hypothesis for Phosphorylation | |
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An Interlude: Reduction Potentials | |
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Maximizing Free Energy and ATP Production | |
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Quantitative Aspects of Mitchell's Chemiosmotic Hypothesis for Phosphorylation | |
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Cellular Structures Involved in the Energy Transduction Process: Similarities among Bacteria, Mitochondria, and Chloroplasts | |
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The Respiratory Chain | |
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The Photosynthetic Electron-Transfer Chain | |
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A Common Underlying Theme in Biological O[subscript 2]/H[subscript 2]O Metabolism: Metalloradical Active Sites | |
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Dioxygen Production: Photosystem II | |
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Introduction | |
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Photosystem II Activity: Light-Catalyzed Two- and Four-Electron Redox Chemistry | |
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Photosystem II Protein Structure and Redox Cofactors | |
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Inorganic Ions of PSII | |
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Modeling the Structure of the PSII Mn Cluster | |
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Proposals for the Mechanism of Photosynthetic Water Oxidation | |
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Oxygen Metabolism | |
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Dioxygen Reactivity and Toxicity | |
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Introduction | |
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Chemistry of Dioxygen | |
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Dioxygen Toxicity | |
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Superoxide Dismutases and Reductases | |
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Introduction | |
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Superoxide Chemistry | |
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Superoxide Dismutase and Superoxide Reductase Mechanistic Principles | |
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Superoxide Dismutase and Superoxide Reductase Enzymes | |
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Peroxidase and Catalases | |
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Introduction | |
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Overall Structure | |
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Active-Site Structure | |
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Mechanism | |
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Reduction of Compounds I and II | |
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Dioxygen Carriers | |
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Introduction: Biological Dioxygen Transport Systems | |
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Thermodynamic and Kinetic Aspects of Dioxygen Transport | |
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Cooperativity and Dioxygen Transport | |
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Biological Dioxygen Carriers | |
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Protein Control of the Chemistry of Dioxygen, Iron, Copper, and Cobalt | |
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Structural Basis of Ligand Affinities of Dioxygen Carriers | |
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Final Remarks | |
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Dioxygen Activating Enzymes | |
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Introduction: Converting Carriers into Activators | |
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Mononuclear Nonheme Metal Centers That Activate Dioxygen | |
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Reducing Dioxygen to Water: Cytochrome c Oxidase | |
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Introduction | |
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Lessons from the X-Ray Structures of Bovine Heart Cytochrome c Oxidase | |
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Reaction Mechanism | |
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Reducing Dioxygen to Water: Multi-Copper Oxidases | |
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Introduction | |
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Occurrence and General Properties | |
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Functions | |
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X-Ray Structures | |
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Structure-Function Relationships | |
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Perspectives | |
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Reducing Dioxygen to Water: Mechanistic Considerations | |
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Hydrogen, Carbon, and Sulfur Metabolism | |
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Hydrogen Metabolism and Hydrogenase | |
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Introduction: Microbiology and Biochemistry of Hydrogen | |
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Hydrogenase Structures | |
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Biosynthesis | |
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Hydrogenase Reaction Mechanism | |
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Regulation by Hydrogen | |
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Metalloenzymes in the Reduction of One-Carbon Compounds | |
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Introduction: Metalloenzymes in the Reduction of One-Carbon Compounds to Methane and Acetic Acid | |
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Electron Donors and Acceptors for One-Carbon Redox Reactions | |
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Conversion to the "Formate" Oxidation Level by Two-Electron Reduction of Carbon Dioxide | |
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Conversion from the "Formate" through the "Formaldehyde" to the "Methanol" Oxidation Level | |
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Interconversions at the Methyl Level: Methyltransferases | |
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Methyl Group Reduction or Carbonylation | |
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Summary | |
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Biological Nitrogen Fixation and Nitrification | |
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Introduction | |
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Biological Nitrogen Fixation: When and How Did Biological Nitrogen Fixation Evolve? | |
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Nitrogen-Fixing Organisms and Crop Plants | |
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Relationships among Nitrogenases | |
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Structures of the Mo-Nitrogenase Component Proteins and Their Complex | |
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Mechanism of Nitrogenase Action | |
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Future Perspectives for Nitrogen Fixation | |
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Biological Nitrification: What Is Nitrification? | |
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Enzymes Involved in Nitrification by Autotrophic Organisms | |
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Nitrification by Heterotrophic Organisms | |
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Anaerobic Ammonia Oxidation (Anammox) | |
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Future Perspectives for Nitrification | |
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Nitrogen Metabolism: Denitrification | |
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Introduction | |
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The Enzymes of Denitrification | |
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Summary | |
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Sulfur Metabolism | |
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Introduction | |
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Biological Role of Sulfur Compounds | |
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Biological Sulfur Cycle | |
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Molybdenum Enzymes | |
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Introduction | |
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The Active Sites of the Molybdenum Enzymes | |
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Molybdenum Enzymes | |
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Conclusions | |
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Tungsten Enzymes | |
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Introduction | |
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Biochemical Properties of Tungstoenzymes | |
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Structural Properties of Tungstoenzymes | |
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Spectroscopic Properties of Tungstoenzymes | |
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Mechanism of Action of Tungstoenzymes | |
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Tungsten Model Complexes | |
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Tungsten versus Molybdenum | |
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Metalloenzymes with Radical Intermediates | |
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Introduction to Free Radicals | |
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Introduction | |
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Free Radical Stability and Reactivity | |
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Electron Paramagnetic Resonance Spectroscopy | |
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Biological Radical Complexes | |
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Cobalamins | |
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Introduction | |
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Nomenclature and Chemistry | |
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Enzyme Systems Using AdoCbl | |
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Unresolved Issues in AdoCbl Requiring Enzymes | |
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MeCbl Using Methionine Synthase as a Case Study | |
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Unresolved Issues in Methyl Transfer Reactions with MeCbl | |
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Ribonucleotide Reductases | |
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Introduction: Three Classes of Ribonucleotide Reductases | |
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Mechanisms of Radical Formation | |
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Conclusions | |
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Fe-S Clusters in Radical Generation | |
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Introduction | |
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Glycyl Radical Generation | |
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Isomerization Reactions | |
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Cofactor Biosynthesis | |
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DNA Repair | |
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Radical-SAM Enzymes: Unifying Themes | |
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Galactose Oxidase | |
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Introduction | |
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Active Site Structure | |
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Oxidation-Reduction Chemistry | |
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Catalytic Turnover Mechanism | |
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Mechanism of Cofactor Biogenesis | |
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Amine Oxidases | |
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Introduction | |
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Structural Characterization | |
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Structure-Function Relationship | |
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Mechanistic Considerations | |
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Biogenesis of Amine Oxidases | |
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Conclusion | |
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Lipoxygenase | |
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Introduction | |
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Structure | |
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Mechanism | |
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Kinetics | |
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Metal Ion Receptors and Signaling | |
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Metalloregulatory Proteins | |
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Introduction: Structural Metal Sites | |
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Structural Zn Domains | |
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Metal Ion Signaling | |
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Metalloregulatory Proteins | |
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Metalloregulation of Transcription | |
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Metalloregulation of Post-Transcriptional Processes | |
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Post-Translational Metalloregulation | |
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Structural Zinc-Binding Domains | |
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Introduction | |
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Molecular and Macromolecular Interactions | |
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Metal Coordination and Substitution | |
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Zinc Fingers and Protein Design | |
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| |
Calcium in Mammalian Cells | |
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Introduction | |
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Concentration Levels of Ca[superscript 2+] in Higher Organisms | |
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The Intracellular Ca[superscript 2+]-Signaling System | |
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A Widespread Ca[superscript 2+]-Binding Motif: The EF-Hand | |
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Ca[superscript 2+] Induced Structural Changes in Modulator Proteins (Calmodulin, Troponin C) | |
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Ca[superscript 2+] Binding in Buffer or Transporter Proteins | |
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Nitric Oxide | |
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Introduction: Physiological Role and Chemistry of Nitric Oxide | |
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Chemistry of Oxygen Activation | |
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Overview of Nitric Oxide Synthase Architecture | |
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Nitric Oxide Synthase Mechanism | |
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| |
Cell Biology, Biochemistry, and Evolution: Tutorial I | |
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Life's Diversity | |
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Evolutionary History | |
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Genomes and Proteomes | |
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Cellular Components | |
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Metabolism | |
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Fundamentals of Coordination Chemistry: Tutorial II | |
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| |
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| |
Introduction | |
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| |
Complexation Equilibria in Water | |
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The Effect of Metal Ions on the pK[subscript a] of Ligands | |
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Ligand Specificity: Hard versus Soft | |
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Coordination Chemistry and Ligand-Field Theory | |
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Consequences of Ligand-Field Theory | |
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Kinetic Aspects of Metal Ion Binding | |
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Redox Potentials and Electron-Transfer Reactions | |
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Abbreviations | |
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Glossary | |
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| |
The Literature of Biological Inorganic Chemistry | |
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| |
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Introduction to the Protein Data Bank (PDB) | |
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Index | |