Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures

BMC Structural Biology

Table 5 Atomic displacement parameter

Base	Atoms of paired bases	Atoms of unpaired bases	Oxygen atoms of water molecules outside clusters	Oxygen atoms of water molecules inside clusters
Adenine	0.393 ± 0.005	0.798 ± 0.010	1.09 ± 0.04	0.95 ± 0.13 (W1) 1.63 ± 0.15 (W2) 1.21 ± 0.11 (W3) 1.96 ± 0.16 (W4) 1.68 ± 0.15 (W5)
Guanine	0.342 ± 0.003	0.827 ± 0.014	1.20 ± 0.05	1.31 ± 0.19 (W1) 1.39 ± 0.18 (W2) 1.59 ± 0.28 (W3) 1.73 ± 0.17 (W4) 0.71 ± 0.12 (W5) 1.36 ± 0.28 (W6) 1.61 ± 0.15 (W7)
Uracil	0.350 ± 0.005	0.967 ± 0.018	1.07 ± 0.05	0.82 ± 0.13 (W1) 0.91 ± 0.22 (W2) 0.96 ± 0.26 (W3) 1.41 ± 0.41 (W4)
Cytosine	0.384 ± 0.004	0.962 ± 0.020	0.85 ± 0.06	0.70 ± 0.14 (W1) 0.80 ± 0.26 (W2) 1.00 ± 0.21 (W3)

Average normalized B-factors (B^N, equation 7) with their standard deviations, computed for different types of atoms: base atoms belonging to paired nucleotides; base atoms belonging to unpaired nucleotides; oxygen atoms of water molecules that do not belong to clusters; oxygen atoms of water molecules that reside into the clusters described in Table 2.

ISSN: 1472-6807