To characterize the structural features of the quinol oxidation site (the QL site) of the cytochrome bo complex, a heme-copper respiratory oxidase in Escherichia coli, we carried out structure-inhibitory potency analyses using 7 p-benzoquinones and 33 substituted phenols. Their effects on its ubiquinol-1 oxidase activity were compared with those on the cytochrome bd complex in E. coli and on cytochromes o and alpha 1 in Acetobacter aceti. They showed similar structural properties of the QL site, although cytochrome o was more sensitive to 4-cyanophenols, suggesting a specific interaction of the hydrogen bond-accepting cyano group with the binding pocket. Replacing one of the methyl groups of 2,6-dimethyl-p-benzoquinone, which is the most potent competitive inhibitor, with an ethyl group markedly decreased the inhibitory activity, indicating that the QL site specifically recognizes one C = O group with two methyl groups as the ortho-substituents. In substituted phenols, ortho-chlorine substituents were the most effective in recognition, and the electron-withdrawing ability of the para-substituent determined an inhibitory potency, probably by stabilizing an anionic form. Based on these observations, we postulate that the QL site of the cytochrome bo complex asymmetrically recognizes exogenous ligands and that this property accounts for the sequential electron transfer from ubiquinols to the low-spin heme.