The Nature of the Short Oxygen–Oxygen Distance in the Mn₄CaO₆ Complex of Photosystem II Crystals

Abstract

The O···O distance for a typical H-bond is ∼2.8 Å, whereas the radiation-damage-free structures of photosystem II (PSII), obtained using the X-ray free electron laser (XFEL), shows remarkably short O···O distances of ∼2 Å in the oxygen-evolving Mn4CaO5/6 complex. Herein, we report the protonation/oxidation states of the short O···O atoms in the XFEL structures using a quantum mechanical/molecular mechanical approach. The O5···O6 distance of 1.9 Å is reproduced only when O6 is an unprotonated O radical (O•–) with Mn­(IV)3Mn­(III), i.e., the S3 state. The potential energy profile shows a barrier-less energy minimum region when O5···O6 = 1.90–2.05 Å (O•– ↓) or 2.05–2.20 Å (O•– ↑). Formation of such a short O5···O6 distance is not possible when O6 is OH– with Mn­(IV)4. In the case in which the O5···O6 distance is 1.9 Å, it seems likely that the O radical species exists in the oxygen-evolving complex of the XFEL-S3 crystals.

Two Distinct Oxygen-Radical Conformations in the X-ray Free Electron Laser Structures of Photosystem II

“…The reported O5···O6 distances of 1.9–2.1 Å are too short to be a low-barrier H-bond (typically 2.4–2.5 Å), whereas they are too long to be a covalent single bond (O–O, 1.4 Å) or a protonated single bond (O–OH, 1.5 Å). QM/MM calculations indicated that the reported O5···O6 distances of 1.9–2.1 Å are reproduced only when O6 is a deprotonated hydroxyl radical, O •– . The presence of O •– requires Mn­(IV) 3 Mn­(III) for S 3 .…”

“…If Mn­(IV) 4 is assumed for S 3 − instead, O6 must have been either OH – or H 2 O. However, the O5···O6 distances are 2.3–2.4 Å for OH – /H 2 O, which suggests that the original 2F-XFEL structures contain neither protonated water molecule (i.e., OH – and H 2 O) at O6 nor Mn­(IV) 4 …”

“…The PSII atomic coordinates were taken from the XRD (PDB code, 3ARC) and 2F-XFEL-2017 (PDB code, 5WS6) structures. The initial atomic coordinates were generated as done in previous studies . D1-His337 was considered to be protonated .…”

“…QM/MM-optimized geometries that correspond to (a) the −O6-2F-XFEL with OH • at W539 and (b) +O6-2F-XFEL conformations.…”

“…Intriguingly, in the 2F-XFEL-2019 structure, the shortening of the O4···O W539 distance to 2.3 Å (O4···OH • W539 /Mn1­(III) conformation) occurs when the incorporation of O6 is not observed (−O6-2F-XFEL conformation), whereas the shortening of the O5···O6 distance to 1.9 Å (O5···O6 •– /Mn4­(III) conformation) occurs when OH • formation at W539 is not observed (+O6-2F-XFEL conformation) (Table ). The following explanations may be possible for the oxygen radical formations.…”