The x-ray structure of the hydrogenase from Desulfovibrio vulgaris Miyazaki F has been solved at 1.8 Å resolution, and refined to a crystallographic R-factor of 0.229. The high resolution crystal structure enabled us to assign the non-protein ligands to Fe atom in the Ni-Fe site, and revealed the presence of a Mg center. From the nature of the electron density map, stereochemical geometry, and atomic parameters of the refined structure, the most probable candidates for the four ligands have been proposed to be diatomic SO, CO, CN molecules and one sulfur atom.