The geometry of metal–ligand interactions relevant to proteins

Abstract

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 contains crystallographic data from `small-molecule' structures determined by X-ray or neutron diffraction to an accuracy much better than that of most current protein structure determinations. The structures selected have a crystallographic R factor ≤ 0.065 and contain Ca, Mg, Mn, Fe, Cu or Zn interacting with ligands which are analogues of the amino-acid side chains commonly found in proteins; they include carboxylate groups, alcohols, phenolates, thiolates, imidazole groups and also water molecules. For each pair, the mean metal–donor-atom distance, the sample standard deviation and the range of observed values are tabulated, using ∼4500 observations in all. Where practicable, subsets with different coordination numbers and/or oxidation states are given. Also included are inter-bond angles 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 deviations could be easily looked up for the validation of a metalloprotein structure or for use in restrained refinement with low-resolution data.