The assignment of the two substrate water sites of the tetramanganese penta-oxygen calcium (Mn 4 O 5 Ca) cluster of photosystem II is essential for the elucidation of the mechanism of biological O-O bond formation and the subsequent design of bio-inspired water-splitting catalysts. We recently demonstrated using pulsed EPR spectroscopy that one of the five oxygen bridges (μ-oxo) exchanges unusually rapidly with bulk water and is thus a likely candidate for one of the substrates. Ammonia, a water analog, was previously shown to bind to the Mn 4 O 5 Ca cluster, potentially displacing a water/substrate ligand [Britt RD, et al. (1989) J Am Chem Soc 111(10):3522-3532]. Here we show by a combination of EPR and time-resolved membrane inlet mass spectrometry that the binding of ammonia perturbs the exchangeable μ-oxo bridge without drastically altering the binding/exchange kinetics of the two substrates. In combination with broken-symmetry density functional theory, our results show that (i) the exchangable μ-oxo bridge is O5 {using the labeling of the current crystal structure [Umena Y, et al. (2011) Nature 473(7345):55-60]}; (ii) ammonia displaces a water ligand to the outer manganese (Mn A4 -W1); and (iii) as W1 is trans to O5, ammonia binding elongates the Mn A4 -O5 bond, leading to the perturbation of the μ-oxo bridge resonance and to a small change in the water exchange rates. These experimental results support O-O bond formation between O5 and possibly an oxyl radical as proposed by Siegbahn and exclude W1 as the second substrate water.PSII | OEC | water oxidizing complex | water-oxidation | Mn cluster I n oxygenic photosynthesis, light-driven water splitting is catalyzed by the oxygen-evolving complex (OEC) of the membrane bound, pigment-protein complex photosystem II (PSII). The OEC consists of an inorganic tetra-manganese penta-oxygen calcium (Mn 4 O 5 Ca) cluster (1-3) and the nearby redox-active tyrosine residue Y Z (D1-Tyr161) that couples electron transfer from the Mn 4 O 5 Ca cluster to P680, the photo-oxidant of PSII. The cluster resembles a "distorted chair", where the base is formed by an oxygen-bridged (μ-oxo) cuboidal Mn 3 O 4 Ca unit (1) (Fig. 1A). The fourth Mn (Mn A4 ) is located outside of the cuboidal unit and is linked via a μ-oxo-bridged ligation (O4) to one of its corners (Mn B3 ). A second linkage between the outer Mn and the cube is provided by a fifth oxygen O5. The Mn 4 O 5 Ca cluster is also held together by six carboxylate ligands and has only one directly coordinating nitrogen ligand, D1-His332 (Fig. 1B).The OEC cycles through a series of five intermediate states that are known as S states (4) (Fig. 1A): S 0 , S 1 (dark stable), S 2 , S 3 , and S 4 (not yet isolated), where the subscript refers to the number of oxidizing equivalents stored in the OEC through successive electron withdrawals by Y Z • . In the 1.9-Å resolution structure, the S state of the cluster was assigned to be S 1 (1). However, this is unlikely as all Mn-Mn, Mn-Ca, and Mn-O/N distances of the crystal structure are ∼...