The geometry of metal-ligand interactions relevant to proteins

Geometrical data which could be of relevance in the structure determination , structure refinement, assessment or understanding of metalloproteins have been extracted from the Cambridge Structural Database (CSD). The CSD conta ins crystallographic data from 'small-molecule' structures determined by X- ray or neutron diffraction to an accuracy much better than that of most cur rent protein structure determinations. The structures selected have a cryst allographic R factor less than or equal to 0.065 and contain Ca, Mg, Mn, Fe , Cu or Zn interacting with ligands which are analogues of the amino-acid s ide chains commonly found in proteins; they include carboxylate groups, alc ohols, phenolates, thiolates, imidazole groups and also water molecules. Fo r each pair, the mean metal-donor-atom distance, the sample standard deviat ion and the range of observed values are tabulated, using similar to 4500 o bservations in all. Where practicable, subsets with different coordination numbers and/or oxidation states are given. Also included are inter-bond ang les at the ligand donor atom, the orientation of carboxylate and imidazole groups with respect to the metal-donor-atom bond and some other aspects of ligand geometry. Thus, for example, target distances and their standard dev iations could be easily looked up for the validation of a metalloprotein st ructure or for use in restrained refinement with low-resolution data.