Table 1.
Important electronegative sites observed in majority of averaged ECOLI and RAT structures (averages over each 1 ns) and characterized by contour levels of −12 and −14 kT (boldface)
| Name of MIP site | Region | Atoms (ECOLI) | Atoms (RAT) |
|---|---|---|---|
| I | Tetraloop | N3(G2659), N7(A2662) | N3(G4323), N7(A4326) |
| IIa | Tetraloop | Phosphates G2659, A2660, G2661 | Phosphates G4323, A4324, G4325 |
| IIb | Tetraloop | Phosphates C2658, G2659 | Phosphates C4322, G4323 |
| IIc | Tetraloop | Phosphates A2657, C2658 | Phosphates A4321, C4322 |
| IId | Tetraloop/G-bulged A-stack | Phosphates U2656, A2657 | Phosphates U4320, A4321 |
| IIIa | Tetraloop/four-G stack | Phosphates A2662, G2663 | Phosphates A4326, G4327 |
| IIIb | Tetraloop/four-G stack | Phosphates G2663, G2664 | Phosphates G4327, G4328 |
| IIIc | four-G stack | N7,O6(G2663), N7,O6(G2664) | N7,O6(G4327), N7,O6(G4328) |
| IIId | G-bulged A-stack | Phosphates G4328, A4329, O6(G4319) | |
| IV | Flexible region | Phosphates C2652, U2653, O2′(A2654) | Phosphates U4316, C4317, O2′(A4318) |
| IVuc, IVcc | Flexible region | Phosphates C2666, C2667, N3(U2653), O4(U2653) | Phosphates C4331, C4332, N3(U4316), O4(U4316), N3(C4317) |
| IVaa | Flexible region | N1(A4318), phosphate A4330 | |
| V | G-bulged A-stack/flexible region | N3(A2654), N3(G2655) | N3(A4318), N3(G4319) |
| VIa | Flexible region | Phosphates A4330, C4331 | |
| VIb | Flexible region/regular duplex | Phosphates C2667, G2668 |