Fig. 2.

Protein–DNA interactions at the ToxR^cyt/toxTpro and ToxR^cyt/ompUpro structures. (A) Sequence of the ToxR^cyt used in this work, with the residues contacting the DNA highlighted (black background), showing the boundaries of the secondary structure elements and the name of the main DNA-contacting regions. Depiction of the residues interacting with toxT promoter DNA (side chains visible) at the (B) recognition helix region; (C) wing element; (D) ancillary wing loop; (E) beginning of helix α1; and (F) transactivation α2-α3 loop (α-loop). Zoomed regions including solvent molecules (red spheres) show the hydrogen bond (blue dashed lines) and van der Waals (green dashed lines) interactions and distances (black dashed lines) between the DNA and (G) Thr77 and Gln78 and (H) Pro101 and Lys102 of monomer D in the ToxR^cyt/toxT20 structure and (I) Thr77 and Gln78 of monomer W in the ToxR^cyt/tompU19 structure.