Table 2.
Ion-binding sites with inner-shell occupancies above 15% in at least one simulation
| Ion-binding site | Occupancy (%) | Maximum binding time (ns) | ||||||
|---|---|---|---|---|---|---|---|---|
| ECOLI1 | ECOLI2 | RAT1 | RAT2 | ECOLI1 | ECOLI2 | RAT1 | RAT2 | |
| Tetraloop and G-bulged A-stack region | ||||||||
| N7(G2659,G4323) | 84 | 47 | 52 | 83 | 2.6 (12) | 3.0 (9) | 2.0 (9) | 3.4 (11) |
| N7(G2663,G4327), N7(G2664,G4328) | 31 | 6 | 9 | 43 | 1.8 | 0.5 | 0.4 | 0.7 |
| O6(G2655,G4319), O2P(G2664,G4328) | 9 | 9 | 21 | 7 | 0.9 | 0.3 | 0.8 | 0.7 |
| Flexible region | ||||||||
| O4(U2653) | 19 | 9 | x | x | 2.2 | 0.6 | x | x |
| O4(U4316) | x | x | 20 | 21 | x | x | 0.9 | 0.8 |
| O2,N3(C4317) | x | x | 24 | 6 | x | x | 4.4 | 0.8 |
| Duplex region | ||||||||
| N7(G2668) | 52 | 55 | x | x | 1.7 | 1.5 | x | x |
| N7(A2670) | 25 | 23 | x | x | 1.2 | 0.8 | x | x |
| N7(G4333) | x | x | 16 | 12 | x | x | 0.9 | 0.5 |
Occupancies exceeding 20% are in boldface. Maximum binding times represent a period of uninterrupted inner-shell binding while numbers in parentheses indicate a period when an ion was found in the described ion-binding site and the surrounding area (i.e. including fluctuations not exceeding 300 ps). Sites marked by ‘x’ are not observable either in ECOLI or in RAT systems.