Geometry of interaction of metal ions with sulfur-containing ligands in protein structures

Abstract

An analysis of the geometry of binding of metal ions by cysteine a methionine residues in protein structures has been made by using the Protein Data Bank. Metal ions have a distinct mode of binding to each of these residues, and this is independent of the nature of the metal center or the type of protein. Metal ions tend to approach the sulfur of Met roughly 38.degree. from the perpendicular to the plane through atoms C.gamma.-S.delta.-C.epsilon.. For the Cys, the approach direction is such that the M.cntdot..cntdot..cntdot.S.gamma.-C.beta.-C.alpha. torsional angle is about .+-. 90 or 180.degree.. The side-chain conformation of the cysteine residue is affected by the presence of the metal ion; there is a shift from the g+ conformation toward g- and mainly t conformations. When two Cys residues at positions i - 3 and i bind to the same metal center, there appears to be some restriction on the geometry of metal binding by the residue i; for such a residue .chi.1 and M.cntdot..cntdot..cntdot.S.gamma.-C.beta.-C.alpha. angles are likely to be around 60.degree. and 270.degree., respectively. Met and Cys residues coordinating to a metal ion are usually from coil or turn regions of the protein structure.