Crystal structure of bovine heart cytochrome c oxidase at 2.8 Å resolution

Thirteen different polypeptide subunits, each in one copy, five phosphatidyl ethanolamines and three phosphatidyl glycerols, two hemes A, three Cu ions, one Mg ion, and one Zn ion are detectable in the crystal structure of bovine heart cytochrome c oxidase in the fully oxidized form at 2.8 Angstrom resolution. A propionate of hems a, a peptide unit (-CO-NH-), and an imidazole bound to Cu-A are hydrogen-bonded sequentially, giving a facile electron transfer path from Cu-A to heme a. The O-2 binding and reduction site, heme a(3), is 4.7 Angstrom apart from Cu-B. Two possible proton transfer paths from the matrix side to the cytosolic side are located in subunit I, including hydrogen bonds and internal cavities likely to contain randomly oriented water molecules. Neither path includes the O-2 reduction site. The O-2 reduction site has a proton transfer path from the matrix side possibly for protons for producing water. The coordination geometry of Cu-B and the location of Tyr(244) in subunit I at the end of the scalar proton path suggests a hydroperoxo species as the two electron reduced intermediate in the O-2 reduction process.