Theoretical studies of biological nitrogen fixation. Part II. Hydrogen bonded networks as possible reactant and product channels

Detailed molecular graphical analyses of the X-ray structure of the Mo-nitrogenase from Azotobacter vinelandii were carried out in order to describe the FeMo-cofactor and protein interactions in terms of intermolecular close contacts. Two major hydrogen bonded networks were found connecting the FeMo-co with the protein surface through cavities. The longer one starts from the homocitrate ligand attached to the Mo-site of the FeMo-co and ends at the center of the inner protein surface, while the shorter one connects the central six-Fe prism of the FeMo-co with the outer protein surface. We propose these networks as possible reactant and product channels of the substrate fixation and reduction processes, based on their possible mechanistic relevance. PM3 semi-empirical, HF and B3LYP density functional calculations were carried out to study various protonation forms of the homocitrate ligand. The homocitrate ligand along with its first layer of water molecules was modeled systematically. It was found that the X-ray structure can be only reproduced if the hydroxy group of the homocitrate is protonated, otherwise drastic rearrangement of water molecules and conformational changes of the shorter leg carboxyl group occurred. The origin of this extra proton was assumed to be the imidazolato ring of the histidine residue attached to the Mo-site of the FeMo-co. (C) 2000 Elsevier Science B.V. All rights reserved.