Table 2. Hydrogen bonds between residues in the secondary binding site and supercoiled DNA along the total 50 ns and last 20 ns of the main (M) simulation (columns 1 and 2) and along the last 20 ns of replica (R1–4) simulations (columns 3–6).
| M (50 ns) | M (last 20 ns) | R1 (last 20 ns) | R2 (last 20 ns) | R3 (last 20 ns) | R4 (last 20 ns) | |
|---|---|---|---|---|---|---|
| Lys466-Ade267 | 28% | 44% | ||||
| Lys466-Thy268 | 30% | 47% | 60% | 84% | 51% | 33% |
| Lys468-Gua269 | 18% | 36% | 25% | |||
| Lys545-Cyt217 | 30% | 29% | 20% | 26% | ||
| Lys545-Gua218 | 64% | 59% | 95% | 72% | 40% | 92% |
| Lys545-Ade219 | 27% | 65% | 25% | |||
| Lys549-Cyt217 | 41% | 46% | 42% | 20% | 14% | 56% |
| Lys549-Gua218 | 26% | 40% | 52% | 95% | 14% | 44% |