Noncovalent interactions between the second coordination sphere and the active site of [NiFeSe] hydrogenase

Abstract

QM/MM studies on seven truncated models of the oxidized as-isolated state of the [NiFeSe] Hases have been undertaken in order to find out the influence of the residues on the second coordination sphere on the active site. The major interactions of the second coordination sphere with that of the active site concerns hydrogen bonds between the CN ligand and Pro420 and Ala421 residues, weak S⋯N interactions between the Cys_(brdg) and the Sec with the His82 and Arg422 residues. Five types of weak noncovalent interactions between the ligands and the residues in the second coordination sphere are classified based on RGD and QTAIM methods. These residues have been found to affect the electronic structure of the active site as evidenced by the computed IR spectral features. The study reveals that the inclusion of all the residues in the second and the third coordination sphere of the enzyme may not be necessary for an accurate description of the active site features. The non-covalent interactions have been found to be stabilizing the Sec in the conformers.