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.