The crystal structure at 2.8 Angstrom resolution of the four protein subunits containing cytochrome c oxidase from the soil bacterium Paracoccus denitrificans, complexed with an antibody F-v fragment, is described. Subunit I contains 12 membrane-spanning, primarily helical segments and binds haem a and the haem a(3)-copper B binuclear centre where molecular oxygen Is reduced to water. Two proton transfer pathways, one for protons consumed in water formation and one for ’proton pumping’, could be identified. Mechanisms for proton pumping are discussed.