It is known that inactivation of the Mn4CaO5 cluster, the catalytic center of water oxidation in photosystem II (PSII), induces a positive shift of the redox potential (Em) of the primary quinone electron acceptor QA by ∼+150 mV, resulting in suppression of the electron transfer from QA to the secondary quinone acceptor QB. Although the relevance of this Em(QA(-)/QA) shift to the photoprotection of PSII has been debated, its molecular mechanism is still enigmatic from a structural viewpoint because QA is ∼40 Å from the Mn4CaO5 cluster. In this work, we have investigated the influence of Mn depletion on the Em of the non-heme iron, which is located between QA and QB, and its surrounding structure. Electrochemical measurements in combination with Fourier transform infrared (FTIR) spectroscopy revealed that Mn depletion shifts Em(Fe(2+)/Fe(3+)) by +18 mV, which is ∼8 times smaller than the shift of Em(QA(-)/QA). Comparison of the Fe(2+)/Fe(3+) FTIR difference spectra between intact and Mn-depleted PSII samples showed that Mn depletion altered the pKa's of a His ligand to the non-heme iron, most probably the D1-His215 interacting QB, and a carboxylate group, possibly D1-Glu244, coupled with the non-heme iron. It was further shown that Mn depletion influences the C≡N vibration of bromoxynil bound to the QB site, indicative of the modification of the QB binding site. On the basis of these results, we discuss the mechanism of a long-range interaction between the donor and acceptor sides of PSII.