Table 1.
Gibbs energy barriers (in kcal/mol) of the reaction pathways with distinct coordination of the Mg2+ ion in the HDV ribozyme.a
| Coordination of Mg2+ b | QM region c | R | R′ d | TS | P |
|---|---|---|---|---|---|
| [U-1(O2), G25(N7)] | QM_AS | 8.3 | 6.1 | 28.8 | 11.1 |
| [G1(pro-RP), U20(O2), G25(O6)] | QM_U20 | 8.3 | 11.5 | 28.0 | -1.1 |
| [U-1(O2)] | QM_AS | 8.3 | 8.7 | 21.9 | 4.4 |
| [G25(O6), G25N7)] | QM_AS | 8.3 | 4.1 | 18.2 | 2.2 |
| [G1(pro-RP), U20(O2)] | QM_U20 | 8.3 | 4.4 | 17.6 | -9.4 |
| [U-1(O2′), G1(pro-RP), U23(pro-SP)] | QM_PHOS | 8.3 | 3.7 | 15.7 | -4.8 |
| [G1(pro-RP), U23(pro-SP)] | QM_PHOS | 8.3 | 5.0 | 15.6 | -21.2 |
| [U-1(O2), U-1(O2′)] | QM_AS | 8.3 | 7.0 | 14.2 | 1.1 |
a
The energies are calculated at the MPW1K/6-31+G(d,p) level and include all necessary corrections, i.e., the pKa correction for the rare ionization forms of the active site (8.3 kcal/mol, see Methods) with the Gibbs energy estimated using the model reaction (-0.7 and -5.0 kcal/mol for TS and P state, respectively, see ESI†).
b
The active site groups participating in the coordination.
c
QM region used in the particular calculation (see Methods, Fig. 1A).
d
The R′ state contains already deprotonated U-1(2′-O−) group.