Exogenous $Cu^{2+}$ or $Zn^{2+}$ at micromolar concentration had a strong inhibitory effect on detergent-solubilized cytochrome c oxidase. A similar effect was observed when $Cu^{2+}$ was added to vesicular cytochrome c oxidase, although the extent of inhibition was significantly larger for the uncoupled state than for the coupled state. Interestingly, the inhibition by $Zn^{2+}$ was almost negligible for both the coupled and uncoupled states. These results suggest that the binding sites for $Cu^{2+}$ ions are exposed to the extravesicular side. whereas those for $Zn^{2+}$ are exposed to the matrix side. The EPR spectra of bound $Cu^{2+}$ ions at 77 K indicate that each of the first two $Cu^{2+}$ ions is ligated by three or four histidine residues, as evidenced by distinct $^{14}N$ superhyperfine splitting. These $Cu^{2+}$ ions can not be removed readily by EDTA and inhibit the enzyme activity by as much as 80%.