The chloride ion, Cl ؊ , is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn 4Ca cluster. Its detailed location and function have not been identified, however. We substituted Cl ؊ with a bromide ion (Br ؊ ) or an iodide ion (I ؊ ) in PSII and analyzed the crystal structures of PSII with Br ؊ and I ؊ substitutions. Substitution of Cl ؊ with Br ؊ did not inhibit oxygen evolution, whereas substitution of Cl ؊ with I ؊ completely inhibited oxygen evolution, indicating the efficient replacement of Cl ؊ by I ؊ . PSII with Br ؊ and I ؊ substitutions were crystallized, and their structures were analyzed. The results showed that there are 2 anion-binding sites in each PSII monomer; they are located on 2 sides of the Mn 4Ca cluster at equal distances from the metal cluster. Anion-binding site 1 is close to the main chain of D1-Glu-333, and site 2 is close to the main chain of CP43-Glu-354; these 2 residues are coordinated directly with the Mn 4Ca cluster. In addition, site 1 is located in the entrance of a proton exit channel. These results indicate that these 2 Cl ؊ anions are required to maintain the coordination structure of the Mn4Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active. membrane proteins ͉ oxygen evolution ͉ photosynthesis ͉ manganese enzyme P hotosynthetic water oxidation produces the oxygen required for life on the earth and is catalyzed by Photosystem II (PSII), a multiprotein complex with a total molecular mass of 350 kDa (1). The catalytic center for water splitting, i.e., the oxygen-evolving complex (OEC), is located in the membrane surface of the luminal side of thylakoid membranes and is composed of 4 Mn atoms and 1 Ca atom in the protein matrix of PSII. Oxygen is produced from 2 molecules of water by sequential, light-induced electron-abstracting events at the Mn 4 Ca cluster that cycle through the Si states with i ϭ 0-4 (2). One or more Cl Ϫ ions are required for the water oxidation cycle to proceed, a requirement not often found in other biological systems (3, 4). Depletion of Cl Ϫ has been shown to inhibit the S 2 3 S 3 and S 3 3 S 0 transitions (5). The roles of Cl Ϫ proposed for OEC include ligation to Mn or Ca atoms (6-8), regulation of the redox potential of the Mn 4 Ca cluster (9), maintaining a hydrogen bond network (10), and activation of the substrate water (11). In addition, an association of Cl Ϫ with amino acid residues in the Mn coordination shell has been proposed (12, 13).The structure of PSII, including the Mn 4 Ca cluster, has been analyzed by x-ray crystallography (14-17). These studies, together with polarized extended x-ray absorption fine structure (EXAFS) measurements (18), have provided much information about the structure of the Mn 4 Ca cluster. However, they did not provide any information about the number and location of Cl Ϫ ions within the OEC. The inhibition of particular S-state transitions upon depletion of Cl Ϫ has been taken as evidence of the close p...