Cyanide binding to cytochrome c oxidase has been investigated by sequential mixing and rapid scan stopped flow spectroscopy. Double mixing experiments confirm earlier reports that cyanide binds rapidly to partially reduced enzyme species formed in turnover. The absorbance/time/wavelength matrices, captured during the onset of cyanide inhibition of cytochrome c oxidase by rapid scan stopped flow, were analyzed by singular value decomposition and the spectral contributions of the chromophores separated. Examination of the time courses and amplitudes of the spectral signals provide evidence that entry of a single (1-1.3) electron into the enzyme is sufficient to trigger rapid cyanide binding. This electron resides predominantly on the cytochrome a/CuA pair in the inhibited enzyme. In addition, although cytochrome a3 remains oxidized, it does not appear to be the site for the initial inhibitory binding of cyanide. Our data suggest that CuB2+ is the initial binding site.