The mechanism of the chlorination reaction of SyrB2, a representative a-ketoglutarate dependent halogenase, was studied with computational methods. First, a macromolecular model of the Michaelis complex was constructed using molecular docking procedures. Based on this structure, a smaller model comprising the first- and some of the second-shell residues of iron and a model substrate was constructed and used in DFT investigations on the reaction mechanism. Computed relative energies and Mossbauer isomer shifts as well as quadrupole splittings indicate that the two oxoferryl species observed experimentally are two stereoisomers resulting from an exchange of the coordination sites occupied by the oxo and chloro ligands. In principle both Fe-IV=O species are reactive and decay to (FeCl)-Cl-III (OH)/carbon radical intermediates via C-H bond cleavage. In the final rebound step, which is very fast and thus precluding equilibration between the two forms of the radical intermediate, the ligand (oxo or chloro) placed closest to the carbon radical (trans to His235) is transferred to the carbon. For the native substrate (L-Thr) the lowest barrier for C-H cleavage was found for an isomer of the oxoferryl species favoring chlorination in the rebound step. CASPT2 calculations for the spin state splittings in the oxoferryl species support the conclusion that once the Fe-IV=O intermediate is formed, the reaction proceeds on the quintet potential energy surface.