Fig. 3
Specific water molecules align with atoms of the AdiC substrates L-arginine and agmatine. A Water network in the substrate-binding pocket of the 1.7 Å resolution AdiC structure in the outward-open conformation. B Modeled L-arginine in the high-resolution structure based on the agmatine bound outward-open AdiC structure [16]. Water molecules H2O3 and H2O13 are located in the vicinity of the primary amino and Nη1 guanidinium groups nitrogen atoms of L-arginine or agmatine. Water molecules H2O5 and H2O7 are located near the modeled oxygen atoms of the L-arginine carboxyl group. C Comparison of the outward-open conformation with functional water molecules (A) with the L-arginine bound outward-facing, occluded conformation of AdiC-N22A (carbon atoms in green) [14]. Interactions are shown with dashed lines and label in Å. Waters are depicted as orange or gray spheres according to Fig. 2. Amino acids are labeled in the one letter code and when interacting with their main-chain carbonyl oxygen or nitrogen atom additionally labeled with (O) or (N) and colored in blue (A–C) and green (C), whereas amino acids interacting with the side chains are colored in cyan (A–C) and green (C)