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Photosystem II (PSII) is the water-splitting enzyme of oxygenic photosynthesis. Using light energy, PSII catalytically oxidizes two water molecules to fuel downstream metabolism, forming an O-O bond and releasing O2 as a byproduct. The reaction mechanism requires the strategic removal of four protons via conserved hydrogen-bonding networks, but these pathways remain poorly understood. Site-directed mutagenesis has been used to study these pathways and the role of specific side chains, such as Lys317 of the D2 subunit. Previous studies showed that the D2-Lys317Ala substitution, which abolishes the flexible hydrogen-bonding -NH3+ group, resulted in delayed O2 release kinetics and diminished catalytic turnover, suggesting Lys317 has a crucial role in facilitating proton egress. Here, we investigated this proton egress pathway by determining the cryo-EM structure of PSII containing the D2-Lys317Ala substitution at a resolution of 1.97 Å. We observed that four new water molecules fill the space previously occupied by Lys317, but these waters lack specific water-protein interactions, leading to heterogeneity and suboptimal hydrogen bonding. We hypothesize that these waters negatively contribute to the existing hydrogen-bonding network and increase the entropic barrier for proton transfer. Additionally, we observed that a conserved chloride ion (Cl1), which is associated with Lys317, is unexpectedly maintained in D2-Lys317Ala PSII. However, unlike in wild-type, Cl1 has no measured effect on oxygen-evolution rates in D2-Lys317Ala PSII. This suggests that the role of Cl1 is dependent on the Lys317 amino group. These findings provide new insight into proton egress through the Cl1 hydrogen-bonding channel.