The geometry of metal-ligand interactions relevant to proteins. II. Anglesat the metal atom, additional weak metal-donor interactions

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 and precision much better than th at of most current protein structure determinations. Structures of Mg, Mn, Fe, Cu and Zn complexes with ligands whose donor atoms may be only N, O, S or Cl have been selected and analysed in terms of the geometry of the metal coordination group - octahedral, tetrahedral, tetragonal pyramidal etc. Th e r.m.s. deviation of all the interbond angles around the metal atom provid es a measure, delta, of the deviation from ideal geometry. Average values o f delta are tabulated for the different metals in each type of complex. For simple non-chelated complexes of Mn, Fe and Zn, distortions of up to 5 deg rees in octahedral complexes and 10 degrees in tetrahedral complexes are fo und to be normal and seem likely to be a consequence of packing effects, li gand bulk or intramolecular effects. Substantially larger distortions are f ound for some other metals and geometries and are common for chelated compl exes. Brief comments on six-, seven- and eight-coordinate Ca complexes are included. Tables are also presented showing that for four- and five-coordin ate complexes of Zn and Cu it is quite common to rnd additional weakly coor dinated ligands, usually with N or O donor atoms and with M ... N,O distanc es longer than a normal bond length but shorter than a van der Waals contac t, e.g. in the range 2.4-3.0 Angstrom for Zn and 2.6-3.0 Angstrom for Cu. A lthough the contributions to bond valency or bonding energy of such interac tions may not be great, their effect on geometry can be considerable; they can, for example, cause much larger distortions of tetrahedral Zn complexes than indicated above.