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![[Figure 1]](cb5136fig1mag.jpg)
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Figure 1
The procedure for determining DNA hydrated building blocks and their application for hydration prediction. (a) Selected structures from the analyzed data set of crystal structures from the PDB, containing 2727 nonredundant DNA chains (gray cartoon) together with the reported crystal water molecules (red balls). (b) Top: example of an extracted dinucleotide with water molecules closer than dassoc = 4.0 Å. Middle: hydrated building block defined as the reference dinucleotide with the water distribution obtained by transferring all water molecules associated with the dinucleotides of the particular NtC/sequence combination. Bottom: 3D maps of water probability density calculated from the water distribution by Fourier averaging (Schneider et al., 1998  ). Water probability density maps were calculated separately for waters closer than dcalc = 3.4 Å to the base (blue mesh) and to the sugar-phosphate atoms (yellow mesh) of the reference dinucleotide. Peaks in the hydration densities, shown as yellow and cyan spheres, are interpreted as hydration sites (HSs). (c) Water probability density maps calculated for PDB entry 6l75 (Jhan et al., 2021) by overlapping the relevant hydrated building blocks over the crystal DNA structure and performing Fourier averaging. |
![[Figure 1]](cb5136fig1.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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