Tm1631-DNA model after 90 ns of MD.

<p>Reactive phosphate group in DNA is marked with a red asterisk. (a) Tm1631-DNA model, residues that interact with the DNA are marked. (b) Magnified view of the Tm1631-DNA interface. DNA phosphate groups and residues that interact with the DNA are represented as sticks; black dashed lines denote putative hydrogen bonds and salt bridges. (c) and (d) Schematic picture of Tm1631-DNA and endonuclease IV-DNA interactions. Similar residues in Tm1631 and endonuclease IV binding sites are in white and blue ellipses, respectively. Hydrogen bonds with DNA are shown for amino acid side chains (solid black arrows) and backbone atoms (solid cyan arrows). Stacking interactions with DNA nucleotides are dashed black lines.