The Mo(V) state of the molybdoenzyme sulfite oxidase (SO) is paramagnetic and can be studied by electron paramagnetic resonance (EPR) spectroscopy. Vertebrate SO at pH < 7 and pH > 9 exhibits characteristic EPR spectra that correspond to two structurally different forms of the Mo(V) active center referred to as the low-pH (lpH) and high-pH (hpH) forms, respectively. Both EPR forms have an exchangeable equatorial OH ligand, but its orientation in the two forms is different. It has been hypothesized that the formation of the lpH species is dependent upon the presence of chloride. In this work we have prepared and purified samples of wild type and various mutants of human SO that are depleted in chloride. These samples do not exhibit the typical lpH EPR spectrum at low pH, but rather show spectra that are characteristic of the blocked species that contains an exchangeable equatorial sulfate ligand. Addition of chloride to these samples results in the disappearance of the blocked species and the formation of the lpH species. Similarly, if chloride is added before sulfite, the lpH species is formed instead of the blocked one. Qualitatively similar results were observed for samples of sulfite oxidizing enzymes from other organisms that were previously reported to form a blocked species at low pH. However, the depletion of chloride has no effect upon the formation of the hpH species.The sulfite-oxidizing enzymes (SOEs), represented by sulfite oxidase (SO) in vertebrates and plants and sulfite dehydrogenase (SDH) in bacteria, catalyze the oxidation of sulfite to sulfate as represented by generic Eq. 1 (1).(1)In humans SO is essential for normal neonatal neurological development, and inborn deficiencies in SO result in severe physical and neurological disorders and early death (2,3).Reaction (1) is catalyzed by the square-pyramidal oxo-molybdenum active center, which has three equatorial sulfur ligands (one from the conserved cysteinyl side chain, and two from the molybdopterin cofactor), one axial oxo ligand, and an exchangeable equatorial oxo ligand in the solvent accessible pocket of the active site (4, 5). During the proposed catalytic cycle (6), sulfite initially reduces Mo(VI) to Mo(IV). Regeneration of the Mo(VI) state Unlike X-ray crystallography or extended X-ray absorption fine structure (EXAFS) spectroscopy, EPR can detect protons in the vicinity of a paramagnetic center and is able to unequivocally identify specific nuclei through using substitutions by or permutations of magnetic isotopes (e.g., 16 O → 17 O, 35 Cl → 37 Cl, 14 N → 15 N, etc.). Both, continuous wave (CW) and pulsed EPR spectroscopic approaches have been used to establish the effects of pH, anions in the media, and mutations near the active site on the identity and structure of the exchangeable equatorial ligand of the Mo(V) ion. It was found that in the absence of inhibiting anions (e.g., PO 4 3− , AsO 4 3− ), wild type (wt) vertebrate SO can show two distinct types of EPR signals, high-pH (hpH) and low-pH (lpH), corresponding to two ...