A Water Molecule Residing in the Fea33+···CuB2+ Dinuclear Center of the Resting Oxidized as-Isolated Cytochrome c Oxidase: A Density Functional Study

Although the dinuclear center (DNC) of the resting oxidized "as-isolated" cytochrome c oxidase (C c O) is not a catalytically active state, its detailed structure, especially the nature of the bridging species between the Fe a3 3+ and Cu B 2+ metal sites, is still both relevant and unsolved. Recent crystallographic work has shown an extended electron density for a peroxide type dioxygen species (O1-O2) bridging the Fe a3 and Cu B centers. In this paper, our density functional theory (DFT) calculations show that the observed peroxide type electron density between the two metal centers is most likely a mistaken analysis due to overlap of the electron density of a water molecule located at different positions between apparent O1 and O2 sites in DNCs of different C c O molecules with almost the same energy. Because the diffraction pattern and the resulting electron density map represent the effective long-range order averaged over many molecules and unit cells in the X-ray structure, this averaging can lead to an apparent observed superposition of different water positions between the Fe a3 3+ and Cu B 2+ metal sites.