The water-splitting protein, photosystem II, catalyzes the light-driven oxidation of water to dioxygen. The solar water oxidation reaction takes place at the catalytic center, referred to as the oxygen-evolving complex, of photosystem II. During the catalytic cycle, the oxygen-evolving complex cycles through five distinct intermediate states, S0–S4. In this study, we trap the oxygen-evolving complex in the S2 intermediate state by low temperature illumination of photosystem II isolated from three different species, Thermosynechococcus vulcanus, the PsbB variant of Synechocystis PCC 6803 and spinach. We apply two-dimensional hyperfine sublevel correlation spectroscopy to detect weak magnetic interactions between the paramagnetic tetra-nuclear manganese cluster of the S2 state of the OEC and the surrounding protons. We identify five groups of protons that are interacting with the tetra-nuclear manganese cluster. From the values of hyperfine interactions and using the recently reported 1.9 Å resolution X-ray structure of the OEC in the S1 state [Umena et al., Nature, 2011, 473, 55], we discuss the assignments of the five groups of protons and draw important conclusions on the structure of the oxygen-evolving complex in the S2 state. In addition, we conclude that the structure of OEC is nearly identical in photosystem II from Thermosynechococcus vulcanus, the PsbB variant of Synechocystis PCC 6803 and spinach.