In Photosystem II, loop E of the chlorophyll‐binding CP47 protein is located near a redox‐active tyrosine, YD, forming a symmetrical analog to loop E in CP43, which provides a ligand to the oxygen‐evolving complex (OEC). A Glu364 to Gln substitution in CP47, near YD, does not affect growth in the cyanobacterium Synechocystis sp. PCC 6803; however, deletion of the extrinsic protein PsbV in this mutant leads to a strain displaying a pH‐sensitive phenotype. Using thermoluminescence, chlorophyll fluorescence, and flash‐induced oxygen evolution analyses, we demonstrate that Glu364 influences the stability of YD and the redox state of the OEC, and highlight the effects of external pH on photosynthetic electron transfer in intact cyanobacterial cells.