Figure 3.

ARM-1 binding sites on E. coli Mfd from computational docking. (A) Overall view of the crystal structure of E. coli Mfd (PDB ID 2eyq, apo form), with potential ARM-1 (shown in space filling mode with black carbon atoms) binding sites in the N-terminal UvrB homology domain (righ part of the protein, in blue), and central (top part, in green) and C-terminal regions (left part, in red). (B) Overlay of the Mfd apo (PDB ID 2eyq; pink) and holo structures (PDB ID 6x50; green), affording a close-up view of the first two binding sites in the Mfd apo structure: ‘N-terminal’ and ‘central’. The ARM-1 molecule visible in the center is lodged between the RH and WB-adjacent helix that are colored in magenta and dark pink, respectively, in the apo-Mfd structure. This binding mode of ARM-1 potentially precludes unraveling of RH and a shift by the WB-adjacent helix (colored in yellow and orange, respectively) as seen in Mfd holo structure bound to RNAP and DNA. Selected regions and residues are labeled and ATP/Mg²⁺ and RNAP are visible near the lower edge of the image, middle and right, respectively.