A Water Molecule Residing in the Fe(a3)(3+)···Cu(B)(2+) Dinuclear Center of the Resting Oxidized as-Isolated Cytochrome c Oxidase: A Density Functional Study

[Image: see text] Although the dinuclear center (DNC) of the resting oxidized “as-isolated” cytochrome c oxidase (CcO) 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 CcO 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.