Fig. 2
Hydrogen-bonding network formed between trypsin, water and basic inhibitors. The XN structures of trypsin in its complexes with N-amidinopiperidine and benzamidine are shown with protein residues as light brown and ligands as cyan sticks. a, c H atoms in the structures of trypsin complexed with N-amidinopiperidine or benzamidine, respectively. X-ray and neutron 2mFo-DFc maps are shown at the 1.8σ level as orange meshes and transparent gray surfaces surrounded by black outlines, respectively. Corresponding mFo-DFc maps are depicted at 3σ in blue and light green surrounding the site for water W3, which has not been modeled in the structures due to insufficient occupancy. Moreover, neutron mFo-DFc omit maps have been generated after removal of all hydrogens from each ligand and all depicted water molecules. These maps are shown at 5σ for ligand and water deuterons in green. b, d Contacts between trypsin and N-amidinopiperidine or benzamidine, respectively. Individual interactions are represented by yellow dashed lines, which are labeled with the distance between the H-bond donor deuterium and corresponding acceptor atom along with the donor-D∙∙∙acceptor angle. Mulliken charges (red) obtained as the mean from a short QM/MM trajectory are depicted for the amidino groups of both ligands, the attached ring atom and the Asp189 carboxylate
