Table 2 Clusters of water molecules around the unpaired RNA bases
From: Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures
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 |