A Ca(2+) ion is an indispensable element in the oxygen-evolving Mn cluster in photosystem II (PSII). To investigate the structural relevance of Ca(2+) to the Mn cluster, the effects of Sr(2+) substitution for Ca(2+) on the structures and reactions of ligands to the Mn cluster during the S-state cycle were investigated using flash-induced Fourier transform infrared (FTIR) difference spectroscopy. FTIR difference spectra representing the four S-state transitions, S(1) --> S(2), S(2) --> S(3), S(3) --> S(0), and S(0) --> S(1), were recorded by applying four consecutive flashes either to PSII core complexes from Thermosynechococcus elongatus or to PSII-enriched membranes from spinach. The spectra were also recorded using biosynthetically Sr(2+)-substituted PSII core complexes from T. elongatus and biochemically Sr(2+)-substituted PSII membranes from spinach. Several common spectral changes upon Sr(2+) substitution were observed in the COO(-) stretching region of the flash-induced spectra for both preparations, which were best expressed in Ca(2+)-minus-Sr(2+) double difference spectra. The significant intensity changes in the symmetric COO(-) peaks at approximately 1364 and approximately 1418 cm(-)(1) at the first flash were reversed as opposite intensity changes at the third flash, and the slight shift of the approximately 1446 cm(-)(1) peak at the second flash corresponded to the similar but opposite shift at the fourth flash. Analyses of these changes suggest that there are at least three carboxylate ligands whose structures are significantly perturbed by Ca(2+)/Sr(2+) exchange. They are (1) the carboxylate ligand having a bridging or unidentate structure in the S(2) and S(3) states and perturbed in the S(1) --> S(2) and S(3) --> S(0) transitions, (2) that with a chelating or bridging structure in the S(1) and S(0) states and perturbed also in the S(1) --> S(2) and S(3) --> S(0) transitions, and (3) that with a chelating structure in the S(3) and S(0) states and changes in the S(2) --> S(3) and S(0) --> S(1) transitions. Taking into account the recent FTIR studies using site-directed mutagenesis and/or isotope substitution [Chu et al. (2004) Biochemistry 43, 3152-3116; Kimura et al. (2005) J. Biol. Chem. 280, 2078-2083; Strickler et al. (2006) Biochemistry 45, 8801-8811], it was concluded that these carboxylate groups do not originate from either D1-Ala344 (C-terminus) or D1-Glu189, which are located near the Ca(2+) ion in the X-ray crystallographic model of the Mn cluster. It was thus proposed that if the X-ray model is correct, the above carboxylate groups sensitive to Sr(2+) substitution are ligands to the Mn ions strongly coupled to the Ca(2+) ion rather than direct ligands to Ca(2+).