Table II.
Nonbonded (van der Waals + Electrostatic) Interaction Energy (in kcal/mol) Between Four Highly Conserved Polymerase Residues at the Active Site (R615, Y714, Q797, and H829) and the DNA for All Four Model Systems (G:C, G:A, 8oxoG:C, and 8oxoG:A), Averaged Over the Last 2 ns of Our Unconstrained MD Trajectories
| Residue–base interaction | G:C (kcal/mol) | G:A (kcal/mol) | 8oxoG:C (kcal/mol) | 8oxoG:A (kcal/mol) |
|---|---|---|---|---|
| R615-dCTP/dATP | −34.6 (4.8) | −18.9 (2.7) | −34.4 (4.5) | −33.2 (3.6) |
| R615-A(Pn−1) | −17.6 (2.8) | −11.9 (1.9) | −18.8 (3.0) | −15.7 (2.4) |
| Y714-dCTP/dATP | −2.2 (0.9) | −1.6 (0.8) | −4.6 (0.7) | −4.0 (0.9) |
| Y714-G/8oxoG(Tn) | −8.9 (1.2) | −6.8 (1.2) | −2.7 (0.8) | −3.9 (1.2) |
| Q797 –T(Tn−1) | −5.8 (0.8) | −5.2 (1.0) | −2.9 (1.3) | −3.7 (1.2) |
| H829 –A(Pn−1) | −9.3 (1.3) | −5.6 (1.0) | −3.3 (1.2) | −2.5 (1.0) |
| H829 –G(Pn−2) | −4.9 (2.4) | −8.1 (1.7) | −5.5 (2.1) | −5.9 (1.5) |
The standard deviations are given in parenthesis.