Substrate binding sites. A. NADH.

<p>View of the active site with NADH bound in the optimized position found by docking as described in the text. Green, molecular surface of holoWrbA calculated from the 2.05 Å crystal structure (PDB ID 3B6J) after removal of the FMN cofactor. Oxidized FMN is depicted as a skeletal model in atomic colors with cyan carbon, and docked NADH with white carbons for differentiation from FMN. Dashed lines represent the indicated distances in Å between nicotinamide C4 and each indicated electron acceptor site of FMN. <b>B. Mutual exclusivity of NADH and BQ.</b> Viewpoint of the binding cavity as in panel A but slightly zoomed out to better depict the steric environment of the full pocket. Translucent white indicates the molecular surface of NADH in the position identified by docking as in panel A; red indicates the molecular surface of BQ calculated from the 1.99 Å crystal structure of the BQ/WrbA complex (PDB ID 3B6K). The part of each substrate that is occluded by the other is represented by the overlap between the red and translucent white surfaces.