Table 2.
Occupancy (in%) of hydrogen bonds between the residues of the 5′-sequence and the remainder of the ribozyme during the course of 20-ns MD simulations
| 5′-Sequence | Hydrogen bond | Pre-5GAU | Pre-5GAA | Pre-5GAC | Pre-5GAG |
|---|---|---|---|---|---|
| N − 1 | U − 1(N3)–C3(O2P) | 35.27 | – | – | – |
| N − 1(O2′)–G1(O1P) | 6.37 | 96.43 | 90.45 | 15.96 | |
| A − 1(N6)–C3(O2P) | – | 43.25 | – | – | |
| N −1(O2P)–U27(N3) | – | 43.28 | – | – | |
| C − 1(N4)–C3(O2P) | – | – | 76.28 | – | |
| G − 1(N1)–C3(O2P) | – | – | – | 91.8 | |
| G − 1(N2)–C3(O2P) | – | – | – | 69.08 | |
| G − 1(O2P)–A77(N6) | – | – | – | 31.85 | |
| A − 2 | A − 2(O4′)–G − 3(O2′) | 4.92 | 26.52 | – | 30.6 |
| A − 2(N6)–C3(O2P) | – | 15.35 | – | – | |
| A − 2(N6)–C33(O2P) | – | – | 67.92 | – | |
| A − 2(N6)–G76(O2P) | – | – | 2.35 | – | |
| A − 2(N1)–C4(N4) | – | – | – | 16.32 | |
| A − 2(N1)–C3(N4) | – | – | – | 5.78 | |
| G − 3 | G − 3(N7)–C32(N4) | 13.67 | – | – | – |
| G − 3(O6)–C33(N4) | 6.75 | – | – | – | |
| G − 3(N2)–C4(O2P) | – | 47.83 | – | – | |
| G − 3(N1)–C4(O2P) | – | 17.42 | – | – | |
| G − 3(N2)–G6(O2P) | – | – | 40.6 | – | |
| G − 3(O5′)–C7(N4) | – | – | 25.93 | – | |
| G − 3(O2′)–G31(O6) | 3.05 | 7.57 | 22.51 | 16.38 | |
| G − 3(N2)–G6(N7) | – | – | 15.13 | – | |
| G − 3(O2′)–A − 2(O4′) | 4.92 | 26.52 | – | 30.6 | |
| G − 3(N2)–G5(O6) | – | – | – | 23.55 | |
| G − 3(N2)–C32(N3) | 3.84 | 4.95 | 9.84 | 13.05 |