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_a3³⁺ and Cu_B²⁺ 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_a3³⁺ and Cu_B²⁺ metal sites.

中文翻译：

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驻留在静止氧化的分离的细胞色素c氧化酶的Fea33 +···CuB2 +双核中心的水分子：密度泛函研究。

尽管静止的氧化后的“分离态”细胞色素c氧化酶（C c O）的双核中心（DNC）不是催化活性状态，但其详细的结构，尤其是Fe _a3 ³⁺和Cu之间的桥联物种的性质_B ²⁺金属位点仍然是相关且尚未解决的。最近的晶体学研究表明，桥接Fe _a3和Cu _B的过氧化物型双氧物种（O1-O2）的电子密度得到扩展中心。在本文中，我们的密度泛函理论（DFT）计算表明，由于位于表观O1和O2之间不同位置的水分子的电子密度重叠，因此观察到的两个金属中心之间的过氧化物类型电子密度很可能是错误的分析。不同C c O分子的DNC中的O2位置具有几乎相同的能量。由于衍射图谱和所得的电子密度图表示在X射线结构中许多分子和晶胞上平均的有效长程有序，因此这种平均可能导致明显观察到Fe _a3 ³⁺之间不同水位的叠加和Cu _B ²⁺金属位点。