title: Coordination geometries of selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in metalloproteins.
abstract: In order to determine preferred coordination geometries of six divalent cations (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+), two sources of experimental data were exploited: Protein Data Bank and Cambridge Structural Database. Metal-binding sites of approximately 100 metalloproteins and 3000 smaller transition metal complexes were analyzed and classified. The correlation between the geometries of small-molecule crystal structures and the metal-binding sites in metalloproteins was investigated. The abundance of amino acid residues participating in coordination metal-protein bonds of metalloproteins was evaluated. From the performed analysis it follows that the octahedral arrangement is preferred by Co2+ and Ni2+, tetrahedral by Zn2+, square planar by Cu2+, and linear by Hg2+. Cadmium (II) cation tends to bind in both tetrahedral and octahedral arrangements and single coordination geometry cannot be unambiguously ascribed to it.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic. lubos@uochb.cas.cz
authors.forename: L
authors.initials: L
authors.lastname: Rulísek
authors.forename: J
authors.initials: J
authors.lastname: Vondrásek
mesh_terms: D000818:Animals; D001665:Binding Sites; D002413:Cations, Divalent; D018360:Crystallography, X-Ray; D016208:Databases, Factual; D006801:Humans; D008667:Metalloproteins / Q000737:chemistry*; D008670:Metals / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D002413:Cations, Divalent; D008667:Metalloproteins; D008670:Metals