Extended Data Fig. 9. Conformations sampled by D1-Asp61, D2-Glu312, and D2-Lys317.

a. Sticks representation of the Mn₄Ca cluster and neighboring residues (Asp61, Glu65, Glu312 and Lys317) for the two-flash state (S₃ state) of Photosystem II from the crystallographic model of Kern et al. (PDB ID: 6DHO). A Cl⁻ ion as well as two water oxygens are also shown as balls. b. Distributions of distances between Lys317 and the two residues Asp61 and Glu312 sampled along 50 ns of classical MD simulation with both Asp61 and Glu312 deprotonated (simulation for S₁ geometry). c. Scheme of a representative configuration of Asp61, Glu65, Glu312 and Lys317 sampled in the S₁ simulation. In this configuration Lys317 is in close contact with deprotonated Glu312. d. Distributions of distances between Lys317 and the two residues Asp61 and Glu312 sampled along 50 ns of classical MD simulation with deprotonated Asp61 and protonated Glu312 (simulation for S₂). e. Scheme of a representative configuration of Asp61, Glu65, Glu312 and Lys317 sampled in the S₂ simulation. Lys317 strongly interacts with Asp61, while protonated Glu312 interacts with Glu65.