Coordination geometries of selected transition metal ions (Co 2+, Ni 2+, Cu 2+, Zn 2+, Cd 2+, and Hg 2+) in metalloproteins

Abstract

In order to determine preferred coordination geometries of six divalent cations (Co 2+, Ni 2+, Cu 2+, Zn 2+, Cd 2+, and Hg 2+), 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 Co 2+ and Ni 2+, tetrahedral by Zn 2+, square planar by Cu 2+, and linear by Hg 2+. Cadmium (II) cation tends to bind in both tetrahedral and octahedral arrangements and single coordination geometry cannot be unambiguously ascribed to it.