Table 2.
Clusters of water molecules around the unpaired RNA bases
| Base | Cluster | Number of waters | Compact-ness, Å |
Distance to the nearest base atom, Å |
Angle, degrees |
Torsion, degrees |
Non-base atoms creating H-bonds with the cluster |
|---|---|---|---|---|---|---|---|
| Adenine | W1 | 42 | 1.3 | N7-W1 2.6 |
C5-N7-W1 142 |
C6-C5-N7-W1 5 |
OP1, OP2 |
| Adenine | W2 | 43 | 0.9 | N6-W2 3.4 |
C6-N6-W2 161 |
N1-C6-N6-W2 -77 |
isolated |
| Adenine | W3 | 66 | 1.3 | N3-W3 2.8 |
C4-N3-W3 132 |
N9-C4-N3-W3 11 |
W5, O2' |
| Adenine | W4 | 25 | 1.4 | N3-W4 (4.6)* |
C4-N3-W4 93 |
N9-C4-N3-W4 -40 |
O2', O3' |
| Adenine | W5 | 25 | 1.2 | N3-W5 (4.7)* |
C4-N3-W5 156 |
N9-C4-N3-W5 60 |
W3 |
| Guanine | W1 | 26 | 1.3 | N7-W1 2.7 |
C5-N7-W1 135 |
C6-C5-N7-W1 -17 |
W2 |
| Guanine | W2 | 17 | 1.1 | O6-W2 2.7 |
C6-O6-W2 131 |
N1-C6-O6-W2 170 |
W1 |
| Guanine | W3 | 17 | 1.0 | N3-W3 3.1 |
C4-N3-W3 126 |
N9-C4-N3-W3 -6 |
W5, O2' |
| Guanine | W4 | 23 | 0.7 | N3-W4 3.1 |
C4-N3-W4 114 |
N9-C4-N3-W4 50 |
O4' |
| Guanine | W5 | 5 | 0.2 | N2-W5 3.0 |
C2-N2-W5 119 |
N3-C2-N2-W5 -8 |
W3 |
| Guanine | W6 | 20 | 0.6 | N2-W6 3.9 |
C2-N2-W6 123 |
N3-C2-N2-W6 76 |
isolated |
| Guanine | W7 | 44 | 1.0 | O6-W7 (4.4)* |
C6-O6-W7 162 |
N1-C6-O6-W7 -4 |
isolated |
| Uracil | W1 | 17 | 1.1 | O4-W1 2.6 |
C4-O4-W1 127 |
C5-C4-O4-W1 -8 |
isolated |
| Uracil | W2 | 14 | 1.0 | C5-W2 3.7 |
C6-C5-W2 76 |
N1-C6-C5-W2 -101 |
OP2 |
| Uracil | W3 | 14 | 0.9 | O2-W3 3.5 |
C2-O2-W3 132 |
N3-C2-O2-W3 136 |
O2' |
| Uracil | W4 | 12 | 0.8 | N3-W4 2.7 |
C4-N3-W4 122 |
C5-C4-N3-W4 170 |
isolated |
| Cytosine | W1 | 24 | 0.9 | N4-W1 2.9 |
C4-N4-W1 116 |
C5-C4-N4-W1 2 |
W3 |
| Cytosine | W2 | 10 | 0.9 | C5-W2 4.0 |
C6-C5-W2 85 |
N1-C6-C5-W2 -127 |
W3, OP2 |
| Cytosine | W3 | 12 | 0.7 | C5-W3 3.6 |
C6-C5-W3 112 |
N1-C6-C5-W3 -177 |
W1, W2, OP2 |
Each cluster is associated with a name (for example W1); the number of water molecules that it contains; the cluster compactness, defined at the maximal distance of a water molecule from the cluster center; the atom of the base that is the closest to it; the distance from this atom; the angle centered on this atom; the torsional angle that monitors deviation of the cluster from the base plane; and the other atoms that might interact with it.
* Distances that are longer than 4.0 Å are placed in parentheses.