The complex is a large integral membrane protein composed of several metal prosthetic sites and 14 protein subunits in mammals. In mammals, eleven subunits are nuclear in origin, and three are synthesized in the mitochondria. The complex contains two hemes, a cytochrome a and cytochrome a, and two copper centers, the Cu and Cu centers. In fact, the cytochrome a and Cu form a binuclear center that is the site of oxygen reduction. Cytochrome c, which is reduced by the preceding component of the respiratory chain (cytochrome bc1 complex, Complex III), docks near the Cu binuclear center and passes an electron to it, being oxidized back to cytochrome c containing Fe. The reduced Cu binuclear center now passes an electron on to cytochrome a, which in turn passes an electron on to the cytochrome a>-Cu binuclear center. The two metal ions in this binuclear center are 4.5 Å apart and coordinate a hydroxide ion in the fully oxidized state.
Crystallographic studies of cytochrome c oxidase show an unusual post-translational modification, linking C6 of Tyr(244) and the ε-N of His(240) (bovine enzyme numbering). It plays a vital role in enabling the cytochrome a- Cu binuclear center to accept four electrons in reducing molecular oxygen and four protons to water. The mechanism of reduction was formerly thought to involve a peroxide intermediate, which was believed to lead to superoxide production. However, the currently accepted mechanism involves a rapid four-electron reduction involving immediate oxygenoxygen bond cleavage, avoiding any intermediate likely to form superoxide.