Theory of chemical bonds in metalloenzymes. IX. Theoretical study on the active site of the ribonucleotide reductase and the related species

The radical harvesting state of a ribonucleotide reductase R2 subunit (RNRR2) is theoretically investigated at the broken-symmetry DFT level. Recently, a high-resolution X-ray crystallography revealed a precise location of the active site structure of RNR-R2 (Class lb) from C. ammoniagenes, and found a linking water near the tyrosine (Tyr) radical site. In this study, the magnetic interaction between the Tyr radical and the diiron core J _Tyr-Fe is investigated for the first time. Used theoretical model for the active site is composed of diiron core, the Tyr residue, and surrounding side-chain groups. After the geometrical structure optimization of the core structures, the magnetic interaction between the iron centers was calculated to be J_{Fe_Fe} = -77.82 cm^-1, which was comparable to the experimental result of J_{Fe_Fe} = -84 cm_-1. The natural orbital analysis clearly showed that the magnetic interaction between the two iron centers mainly interact through the p orbital of the bridging μ-oxo. It was also calculated that the J_{Tyr_Fe} interaction is negligibly weak, and the Tyr radical is almost in an isolated or a free radical state. These results suggest that the linking water may be used for (1) a confinement of the reactive Tyr radical in the hydrogen bonds or (2) a hydrogen-transfer coupled with electron transfer at the radical formation step of the Tyr.