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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
  1. 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.
  2. * Distances that are longer than 4.0 Å are placed in parentheses.