Density functional theory calculations on the oxygen activation process in cysteine dioxygenase (CDO) and three active site mutants whereby one histidine group is replaced by a carboxylic acid group are reported. The calculations predict an oxygen activation mechanism that starts from an Fe-III-O-O-center dot complex that has close lying singlet, triplet, and quintet spin states. A subsequent spin state crossing to the quintet spin state surfaces leads to formation of a ring-structure whereby an O-S bond is formed. This weakens the central O-O bond, which is subsequently broken to give sulfoxide and an iron-oxo complex. The second oxygen atom is transferred to the substrate after a rotation of the sulfoxide group. A series of calculations were performed on cysteine dioxygenase mutants with a 2His/1Asp motif rather than a 3His motif. These calculations focused on the differences in catalytic and electronic properties of nonheme iron systems with a 3His ligand system versus a 2His/1Asp motif, such as taurine/alpha-ketoglutarate dioxygenase (TauD), and predict why CDO has a 3His ligand system while TauD and other dioxygenases share a 2His/1Asp motif. One mutant (H86D) had the ligand trans to the dioxygen group replaced by acetate, while in another set of calculations the ligand trans to the sulfur group of cysteinate was replaced by acetate (H88D). The calculations show that the ligands influence the spin state ordering of the dioxygen bound complexes considerably and in particular stabilize the quintet spin state more so that the oxygen activation step should encounter a lower energetic cost in the mutants as compared to WT. Despite this, the mutant structures require higher O-O bond breaking energies. Moreover, the mutants create more stable iron-oxo complexes than the WT, but the second oxygen atom transfer to the substrate is accomplished with much higher reaction barriers than the WT system. In particular, a ligand trans to the sulfur atom of cysteine that pushes electrons to the iron will weaken the Fe-S bond and lead to dissociation of this bond in an earlier step in the catalytic cycle than the WT structure. On the other hand, replacement of the ligand trans to the dioxygen moiety has minor effects on cysteinate binding but enhances the barriers for the second oxygen transfer process. These studies have given insight into why cysteine dioxygenase enzymes contain a 3His ligand motif rather than 2His/1Asp and show that the ligand system is essential for optimal dioxygenation activity of the substrate. In particular, CDO mutants with a 2His/1Asp motif may give sulfoxides as byproduct due to incomplete dioxygenation processes.