Understanding the water oxidation mechanism in Photosystem II (PSII) stimulates the design of biomimetic artificial systems that can convert solar energy into hydrogen fuel efficiently. The Sr2+-substituted PSII is active but slower than with the native Ca2+ containing PSII as an oxygen evolving catalyst. Here, we use Density Functional Theory (DFT) to compare the energetics of the S2 to S3 transition in the Mn4O5Ca2+ and Mn4O5Sr2+ clusters. The calculations show that deprotonation of the water bound to Ca2+ (W3), required for the S2 to S3 transition, is energetically more favorable in Mn4O5Ca2+ than Mn4O5Sr2+. In addition, we have calculated the pKa of the water that bridges Mn4 and the Ca2+/Sr2+ in the S2 state using continuum electrostatics. The calculations show that the pKa is higher by 4 pH units in the Mn4O5Sr2+cluster.