Fig. 4: Structural changes in select regions of the water and proton channels of PS II during the S₃→S₀ transition.

a, The terminus of the O1 channel near the OEC that includes the group of five waters (W26–W30) in this region. Overlaid is the 2mF_obs− DF_calc electron density map contoured at 0.8σ, 1.0σ and 1.5σ. b, The O4 and Cl1 channels (branch A) that include the D1-D61 and D1-E65/D2-E312 region that is suggested to function as a proton gate. Overlaid are mF_obs− DF_calc omit maps for W1, W2 and D61 shown at 2.5σ, 3.0σ and 4.0σ. Also shown is the F_obs(time point) − F_obs(2F) difference density map within a 1.5-Å radius of W19/W20/W48 in the O4 channel at 3σ (orange map). The observed rotation angle at the side chain of E65 at particular time points is calculated with respect to the corresponding side chain position at the 2F state. Major changes are highlighted with an arrow or dashed circle. All waters are coloured by their B factors according to the diverging colour scheme shown in the figure. Important hydrogen-bond interactions are shown with a binary colour scheme to indicate strength (distance < 2.8 Å is red and 2.8–3.2 Å is gray).