Figure 4.

A closer look at the central and the top portions of the DNC model clusters studied here. Our recent calculations⁶¹ have shown that the two water molecules HOH604 and HOH608 found near the DNC in the X-ray crystal structure 3S8G are likely to shift to the top of the water cluster (see Top Cluster II) during the P_R → F transition. Therefore, in A, Peroxo, Hydroperoxo, P_M and P_R states, these two water molecules are within the DNC and the top portion of each cluster with the H-bonding interactions is shown in “Top Cluster I”. In the following states F, F_H, and O_H, these two water molecules are shifted to the top of the cluster as shown in “Top Cluster II”. Our previous pK_a calculations^54,61 have indicated that the His376 side chain is likely in the cationic protonated state in these DNC clusters, and the Tyr237 side chain is in neutral protonated state in A and Peroxo intermediates, and in ionic deprotonated state in Hydroperoxo, P_R, F, F_H, and O_H intermediates (the proton on the heme-a₃ farnesyl hydroxyl group is rotated to have H-bonding interaction with the Tyr237⁻ side chain). In P_M, the Tyr237 side chain is in the Tyr237-O^• radical state. The rest of each model is similar to what was shown in Figure 3.