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Simple Summary: Many biological systems contain iron–sulfur clusters, which are typically found as components of electron transport proteins. Continuum electrostatic calculations were used to investigate the effect of protein environment on the redox properties of the three iron–sulfur clusters in the cyanobacterial photosystem I. Our results show a good correlation between the estimated and the measured reduction potential. Moreover, the results indicate that the low potential of FX is shown to be due to the interactions with the surrounding residues and ligating sulfurs. Our results will help in understanding the electron transfer reaction in photosystem I. Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron–sulfur cluster FX, which is followed by two terminal iron–sulfur clusters FA and FB. Experiments have shown that FX has lower oxidation potential than FA and FB, which facilitates the electron transfer reaction. Here, we use density functional theory and Multi-Conformer Continuum Electrostatics to explain the differences in the midpoint E m potentials of the FX, FA and FB clusters. Our calculations show that FX has the lowest oxidation potential compared to FA and FB due to strong pairwise electrostatic interactions with surrounding residues. These interactions are shown to be dominated by the bridging sulfurs and cysteine ligands, which may be attributed to the shorter average bond distances between the oxidized Fe ion and ligating sulfurs for FX compared to FA and FB. Moreover, the electrostatic repulsion between the 4Fe-4S clusters and the positive potential of the backbone atoms is lowest for FX compared to both FA and FB. These results agree with the experimental measurements from the redox titrations of low-temperature EPR signals and of room temperature recombination kinetics. [ABSTRACT FROM AUTHOR]