A study is presented on the effect of zinc binding at the matrix side, on the proton pump of purified liposome reconstituted bovine heart cytochrome c oxidase (COV). Internally trapped Zn2+ resulted in 50% decoupling of the proton pump at level flow. Analysis of the pH dependence of inhibition by internal Zn2+ of proton release in the oxidative and reductive phases of the catalytic cycle of cytochrome c oxidase indicates that Zn2+ suppresses two of the four proton pumping steps in the cycle, those taking place when the 2 OH− produced in the reduction of O2 at the binuclear center are protonated to 2 H2O. This decoupling effect could be associated with Zn2+ induced conformational alteration of an acid/base cluster linked to heme a3.