Fig. 7: Spatial boundaries, occupancy, and water exchange in the water wheel region.
a Water distributions and MD conformations around residue N298 (wild-type, blue) and A298 (N298A mutant, red) are represented by extracting 40 snapshots by each of the 10 independent 400 ns-long trajectories. Water wheel molecules were selected within a 3.8 Å-radius sphere centered on the center of mass of the Cα atoms of residues V185, H190, L343, A344, CP43-A386, and CP43-I398. Red and blue dots and lines represent water molecules and residues. A less frequently sampled cluster in the upper left identifies a third, alternative water binding site on the calcium, consistent with recent structural data for T. vestitus24 (see Supplementary Fig. 20). Yellow spheres indicate the five waters of the pentagon, and W3 and W4 from a cryo-EM structure (PDB ID: 7N8O, Synechocystis sp. PCC 6803)64. MD snapshots were fitted to this structure using the backbone atoms of D1-protein residues 165–210, 303–344, and CP43-protein residues 366–418. b The cavity boundaries for wild-type (blue) and N398A (red) were defined using a central 6 Å sphere centered on the water wheel, and an outer 4.5 Å-radius sphere centered on the Mn4Ca cluster; see Supplementary Information for details. c Histograms of the water occupancy for the “water wheel” within the 3.8 Å-radius spherical region (detailed in panel a) for wild-type (blue) and N298A (red). d The Mn4CaO5-6 cluster and its surrounding environment, including waters W3, W4 (calcium-bound), W26–W30 (water wheel), and selected residues. We analyzed the water exchange between the cyan 3.0 Å-radius sphere centered on the Ca and the red 3.8 Å-radius sphere centered on the water wheel cluster. Table reports the probability of water transitions from the red to the cyan sphere, estimated from transition events within consecutive 10 ps intervals.
