Background: Photosystem II, the water-splitting enzyme, includes a protein, D1, which can be coded by three different psbA genes in Thermosynechococcus elongatus. Results: In PsbA2-PSII, the environment of Tyr Z is different from that in PsbA1-PSII and PsbA3-PSII. Conclusion: The geometry of the Tyr Z -O⅐⅐⅐H⅐⅐⅐N⑀-His-190 bonding is an important parameter for PSII activity. Significance: The environment of the cofactors is involved in the tuning of the electron transfer efficiency.