Fig. 4. NM102 docking in the ATP binding site of Mfd.

A Upper part: strip of the eight domains with the following color code blue D1a-D2-D1b, orange D3, pink D4, yellow D5, green D6, and red D7. Lower part: Mfd rendered surfaces of conformations L₀ inactive (pdb id 2eyq) and L₁ active (pdb id 6 × 26), and their corresponding view at 90°. The color code of the surface corresponds to the strip of domains shown above. Right part, top insert: Close-up of Mfd from E. coli with the docking of ATP (in stick with carbon colored in cyan) and down insert: similar view with NM102 (in stick with carbon colored in deepteal). The residues involved in the sphere of binding of ligands are shown as sticks. The color code of the domains is respected with residues of D5 and D6 in yellow and green, respectively, and residues of motifs I and II in red and blue, respectively. B Close-up of the docking of ATP (cyan sticks) and NM102 (orange stick) in Mfd of E. coli harboring the site-directed mutations F597A, F599A, K634A, and E730Q. For the sake of comparison, position of ATP in the non-mutated Mfd is shown as black lines.