Cytochrome c oxidase contains a binding site for a non-redox-active metal at the interface of subunits I and II, usually a magnesium ion. In Paracoccus denitrificans oxidase, typically 20% may be replaced by manganese, using standard growth media. Site-directed mutants were constructed in subunit II (D193N and E218Q), and the isolated enzymes analyzed by total-reflection X-ray fluorescence spectrometry and EPR. Both mutants show a strong reduction of the manganese stoichiometry and a diminished electron transfer activity, demonstrating that D193 and E218 are involved in the binding of a manganese/magnesium ion in this site.