Fig. 5.

Protein-DNA hydrogens bonds involved in the structure models of the N-NTD:DNA complex. Count of protein-DNA hydrogen bonds with persistency higher that 10% were with respect to amino acid (magenta bars) and nucleotide residues (green and blue bars) for the interaction of the N-NTD with (A) dsTRS, (B) dsNS, (C) ssTRS(+), (D) ssNS(+), (E) ssTRS(−), and (F) ssNS(−). The residues involved in the persistent protein-DNA hydrogen bonds (green sphere) and salt bridges (orange sphere) are indicated on the representative structural models of the (G) N-NTD:dsTRS and (H) N-NTD:ssTRS(−) complex. The protein is shown as a cartoon model in gray and DNA as a cartoon-ring model in light pink with TTT motif in magenta. (I) The most recurrent residues (R92, R107, Y172, and R177) involved in protein-DNA hydrogen bonds are indicated as blue spheres on the N-NTD structure. The protein is shown as a cartoon model with the β-sheet I (β2/β3/β4), β-sheet II (β1/β5), and α-helices (α1 and α2) colored in cyan, orange, and magenta, respectively.