Herbicides that target photosystem II (PSII) compete with the native electron acceptor plastoquinone for binding at the Q B site in the D1 subunit and thus block the electron transfer from Q A to Q B . Here, we present the first crystal structure of PSII with a bound herbicide at a resolution of 3.2 Å . The crystallized PSII core complexes were isolated from the thermophilic cyanobacterium Thermosynechococcus elongatus. The used herbicide terbutryn is found to bind via at least two hydrogen bonds to the Q B site similar to photosynthetic reaction centers in anoxygenic purple bacteria. Herbicide binding to PSII is also discussed regarding the influence on the redox potential of Q A , which is known to affect photoinhibition. We further identified a second and novel chloride position close to the water-oxidizing complex and in the vicinity of the chloride ion reported earlier (Guskov, A., Kern, J., Gabdulkhakov, A., Broser, M., Zouni, A., and Saenger, W. (2009) Nat. Struct. Mol. Biol. 16, 334 -342). This discovery is discussed in the context of proton transfer to the lumen.The process of photosynthesis converts solar energy into biochemically amenable energy. A distinction is made between oxygenic and anoxygenic photosynthesis. In the latter sulfur compounds, hydrogen gas or organic materials serve as electron source. In contrast, oxygenic photosynthesis in higher plants, algae, and cyanobacteria uses water as an electron source and generates molecular oxygen, thereby maintaining the level of oxygen in the atmosphere. Water oxidation takes place at the large homodimeric protein-cofactor complex photosystem II (PSII), 7 a light-driven water:plastoquinone oxidoreductase harbored in the thylakoid membrane (1-3). The structure of the PSII core complex (PSIIcc) from the thermophilic cyanobacterium Thermosynechococcus elongatus is known from x-ray crystallographic studies at a current resolution of 2.9 Å (4, 5). The photochemical reaction center (RC) in PSII is of type II and structurally related to the RC of purple bacteria (pbRC) (6), which perform anoxygenic photosynthesis. The PSII-RC contains four chlorophyll a (Chla) molecules (P D1 , P D2 , Chl D1 , and Chl D2 ), two pheophytins (Pheo D1 and Pheo D2 ), and two plastoquinones (PQ) (Q A and Q B ) with a nonheme iron in between. These cofactors are embedded in a heterodimeric protein matrix formed by subunits D1 and D2 (systematic names: PsbA and PsbD, respectively) and are arranged in two pseudo-C2 symmetric branches with respect to a 2-fold rotation axis, which crosses the non-heme iron and is oriented normal to the membrane plane.Photons from sunlight are collected by antenna proteins of PSII, and the excitation energy is transferred to the RC, where it gives rise to the formation of the radical pair P D1 ⅐ϩ Pheo D1 ⅐Ϫ and subsequent electron transfer to the fixed single-electron transmitter Q A . The electron hole at P D1 ⅐ϩ is able to abstract electrons via the redox-active tyrosine Y Z (Tyr-161A) from the heteronuclear Mn 4 Ca cluster located at the lumenal (d...