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Journal ArticleDOI

Structural and Functional Aspects of Metal Sites in Biology

07 Nov 1996-Chemical Reviews (American Chemical Society)-Vol. 96, Iss: 7, pp 2239-2314
TL;DR: The authors present here a classification and structure/function analysis of native metal sites based on these functions, and the coordination chemistry of metalloprotein sites and the unique properties of a protein as a ligand are briefly summarized.
Abstract: For present purposes, a protein-bound metal site consists of one or more metal ions and all protein side chain and exogenous bridging and terminal ligands that define the first coordination sphere of each metal ion. Such sites can be classified into five basic types with the indicated functions: (1) structural -- configuration (in part) of protein tertiary and/or quaternary structure; (2) storage -- uptake, binding, and release of metals in soluble form: (3) electron transfer -- uptake, release, and storage of electrons; (4) dioxygen binding -- metal-O{sub 2} coordination and decoordination; and (5) catalytic -- substrate binding, activation, and turnover. The authors present here a classification and structure/function analysis of native metal sites based on these functions, where 5 is an extensive class subdivided by the type of reaction catalyzed. Within this purview, coverage of the various site types is extensive, but not exhaustive. The purpose of this exposition is to present examples of all types of sites and to relate, insofar as is currently feasible, the structure and function of selected types. The authors largely confine their considerations to the sites themselves, with due recognition that these site features are coupled to protein structure at all levels. In themore » next section, the coordination chemistry of metalloprotein sites and the unique properties of a protein as a ligand are briefly summarized. Structure/function relationships are systematically explored and tabulations of structurally defined sites presented. Finally, future directions in bioinorganic research in the context of metal site chemistry are considered. 620 refs.« less

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Journal ArticleDOI
TL;DR: Copper sites have historically been divided into three classes based on their spectroscopic features, which reflect the geometric and electronic structure of the active site: type 1 or blue copper, type 2 (T2) or normal copper, and type 3 (T3) or coupled binuclear copper centers.
Abstract: Copper is an essential trace element in living systems, present in the parts per million concentration range. It is a key cofactor in a diverse array of biological oxidation-reduction reactions. These involve either outer-sphere electron transfer, as in the blue copper proteins and the Cu{sub A} site of cytochrome oxidase and nitrous oxide redutase, or inner-sphere electron transfer in the binding, activation, and reduction of dioxygen, superoxide, nitrite, and nitrous oxide. Copper sites have historically been divided into three classes based on their spectroscopic features, which reflect the geometric and electronic structure of the active site: type 1 (T1) or blue copper, type 2 (T2) or normal copper, and type 3 (T3) or coupled binuclear copper centers. 428 refs.

3,241 citations

Journal ArticleDOI
04 Dec 1998-Science
TL;DR: A three-dimensional structure for the monomeric iron-containing hydrogenase (CpI) from Clostridium pasteurianum was determined, providing insights into the mechanism of biological hydrogen activation and has broader implications for [Fe-S] cluster structure and function in biological systems.
Abstract: A three-dimensional structure for the monomeric iron-containing hydrogenase (CpI) from Clostridium pasteurianum was determined to 1.8 angstrom resolution by x-ray crystallography using multiwavelength anomalous dispersion (MAD) phasing. CpI, an enzyme that catalyzes the two-electron reduction of two protons to yield dihydrogen, was found to contain 20 gram atoms of iron per mole of protein, arranged into five distinct [Fe-S] clusters. The probable active-site cluster, previously termed the H-cluster, was found to be an unexpected arrangement of six iron atoms existing as a [4Fe-4S] cubane subcluster covalently bridged by a cysteinate thiol to a [2Fe] subcluster. The iron atoms of the [2Fe] subcluster both exist with an octahedral coordination geometry and are bridged to each other by three non-protein atoms, assigned as two sulfide atoms and one carbonyl or cyanide molecule. This structure provides insights into the mechanism of biological hydrogen activation and has broader implications for [Fe-S] cluster structure and function in biological systems.

1,719 citations

Journal ArticleDOI
01 Aug 1997-Science
TL;DR: Iron-sulfur clusters now rank with such biological prosthetic groups as hemes and flavins in pervasive occurrence and multiplicity of function.
Abstract: Iron-sulfur proteins are found in all life forms. Most frequently, they contain Fe2S2, Fe3S4, and Fe4S4 clusters. These modular clusters undergo oxidation-reduction reactions, may be inserted or removed from proteins, can influence protein structure by preferential side chain ligation, and can be interconverted. In addition to their electron transfer function, iron-sulfur clusters act as catalytic centers and sensors of iron and oxygen. Their most common oxidation states are paramagnetic and present significant challenges for understanding the magnetic properties of mixed valence systems. Iron-sulfur clusters now rank with such biological prosthetic groups as hemes and flavins in pervasive occurrence and multiplicity of function.

1,677 citations

References
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Journal ArticleDOI
TL;DR: The effective ionic radii of Shannon & Prewitt [Acta Cryst. (1969), B25, 925-945] are revised to include more unusual oxidation states and coordinations as mentioned in this paper.
Abstract: The effective ionic radii of Shannon & Prewitt [Acta Cryst. (1969), B25, 925-945] are revised to include more unusual oxidation states and coordinations. Revisions are based on new structural data, empirical bond strength-bond length relationships, and plots of (1) radii vs volume, (2) radii vs coordination number, and (3) radii vs oxidation state. Factors which affect radii additivity are polyhedral distortion, partial occupancy of cation sites, covalence, and metallic character. Mean Nb5+-O and Mo6+-O octahedral distances are linearly dependent on distortion. A decrease in cation occupancy increases mean Li+-O, Na+-O, and Ag+-O distances in a predictable manner. Covalence strongly shortens Fe2+-X, Co2+-X, Ni2+-X, Mn2+-X, Cu+-X, Ag+-X, and M-H- bonds as the electronegativity of X or M decreases. Smaller effects are seen for Zn2+-X, Cd2+-X, In2+-X, pb2+-X, and TI+-X. Bonds with delocalized electrons and therefore metallic character, e.g. Sm-S, V-S, and Re-O, are significantly shorter than similar bonds with localized electrons.

51,997 citations

Journal ArticleDOI
TL;DR: The demonstration that O2·- can reduce ferricytochrome c and tetranitromethane, and that superoxide dismutase, by competing for the superoxide radicals, can markedly inhibit these reactions, is demonstrated.

12,468 citations

Journal ArticleDOI
TL;DR: "It is certain that all bodies whatsoever, though they have no sense, yet they have perception, and whether the body be alterant or alterec, evermore a perception precedeth operation; for else all bodies would be like one to another."

8,157 citations

Journal ArticleDOI
TL;DR: The Protein Data Bank is a computer-based archival file for macromolecular structures that stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies.

7,983 citations

Journal ArticleDOI
TL;DR: In this paper, the electron transfer reactions between ions and molecules in solution have been the subject of considerable experimental study during the past three decades, including charge transfer, photoelectric emission spectra, chemiluminescent electron transfer, and electron transfer through frozen media.

7,155 citations