Structure of hydrogenase from sulfate-reducing bacteria and cytochrome c' from photosynthetic bacteria are described. Hydrogenase from Desulfovibrio vulgaris Miyazaki F has four active sites including metal atoms. They are [Fe4-S4], [Fe3-S4], [Fe4-S4], and [Ni-Fe]. Additional Mg center is also found. The structure of n-butylisocyanide-bound Rhodobacter capsulatus cytochrome c', a first example of ligand bound structure of cytochrome c', has been determined and compared with that of the native protein. There are significant conformational changes of amino acid residues in the heme vicinity, accompanied by a rearrangement of the hydrogen bonding pattern, is observed. The results suggest that rearrangements as a consequence of ligand binding could drive dimer dissociation in some species and the heme propionate may participate in proton transfer.