Fig. 9
View of the PRO-GLH-C model (8 ns, the same snapshot as in Fig. 8) showing water traps. Protein and DNA residues coordinating the water molecule (red ball) are shown as a stick model and colored according to atom type (green, C; blue, N; red, O; orange, P). Other parts of the complex are either shown as a cartoon model or hidden for clarity. Distances between possible hydrogen bond donors and acceptors are indicated by dashed lines. a, Glu2, Glu5, and oxoG0. b, schematic representation of hydrogen bonds formed by the water molecule (blue dot) trapped between Glu2, Glu5, and oxoG0. The numbers indicate percentage of snapshots in which the bond is observed, averaged over all GLU models (top) or GLH models (bottom). c, Arg260, Gly261, oxoG0 and T+1. d, Glu76, Arg109, and oxoG0