Explaining the Different Geometries of the Water Oxidising Complex in the Nominal S3 State Crystal Structures of Photosystem II at 2.25 Å and 2.35 Å

: Recently two atomic resolution crystal structures of Photosystem II, in the double flashed, nominal S3 intermediate state of its Mn4 Ca water oxidising complex (WOC), have been presented (Young et al., Nature 2016, 540, 453; Suga et al., Nature 2017, 543, 131). These structures are at 2.25 A and 2.35 A resolution, respectively. Although highly similar in most respects, the structures differ in a key region within the WOC catalytic site. In the 2.25 A structure, one oxy species (O5) is observed within the WOC cavity, weakly associated with the Mn centres, similar to that seen earlier in the 1.95 A XRD structure of the S1 intermediate (Suga et al., Nature, 2015, 517, 99). In the 2.35 A structure, two such species are seen (O5, O6), with the Mn centres and O5 positioned as in the 2.25 A structure and an O5-O6 separation of ∼1.5 A, consistent with peroxo formation. This suggests O5 and O6 are substrate water derived species in this double flashed form. Recently we have presented (Petrie, et al., Chem. Phys. Chem., 2017) a large scale (220 atom) quantum chemical model of the Young et al. 2.25 A structure, which quantitatively explains all significant features within the WOC region of that structure, particularly the positions of the metal centres and O5 group. Critical to this was our assumption of a 'low' Mn oxidation paradigm (mean S1 Mn oxidation level of +3.0, Petrie et al., Angew. Chem. Int. Ed., 2015), rather than a 'high' oxidation model (mean S1 oxidation level of +3.5), widely assumed in the literature. Here we show that our same oxidation state model predicts two classes of energetically close S3 structural forms, analogous to the S1 state, one with the metal centres and O5 positioned as in the 2.25 A structure, and the other with the metals similarly placed, but with O5 located in the O6 position of the 2.35 A structure. We show that the Suga et al. 2.35 A structure is likely a superposition of two such forms, one from each class, which is consistent with reported atomic occupancies for that structure and the relative total energies we calculate for the two structural forms.