The crystal structure of photosystem IT (PSII) analyzed at a resolution of 1.9 A revealed a remarkably short H-bond between redox-active tyrosine Y-z and D1-His190 (2.46 angstrom donor-acceptor distance). Using large-scale quantum mechanical/molecular mechanical (QM/MM) calculations with the explicit PSII protein environment, we were able to reproduce this remarkably short H-bond in the original geometry of the crystal structure in the neutral [YzO center dot center dot center dot H center dot center dot center dot N-e-His-N delta H center dot center dot center dot O=Asn] state, but not in the oxidized states, indicating that the neutral state was the one observed in the crystal structure. In addition to the appropriate redox/protonation state of Y-z and D1-His190, we found that the presence of a cluster of water molecules played a key role in shortening the distance between Y-z and D1-His190. The orientations of the water molecules in the cluster were energetically stabilized by the highly polarized PSII protein environment, where the Ca ion of the oxygen-evolving complex (OEC) and the OEC ligand D1-Glu189 were also involved.