Fig. 4: Structural and mechanistic studies of SNAr 1.3.
From: Engineered enzymes for enantioselective nucleophilic aromatic substitutions
a, SNAr1.3 crystals soaked with iodide (pink sphere) reveal a halide binding site composed of side chain and backbone interactions with residues M64, R65, R124, D125 and P128 (blue sticks). Anomalous map contoured at 14σ (pink mesh). Arg124 is shown as transparent, as it was not visible in the electron density owing to side chain conformational heterogeneity. b, SNAr1.3 crystals soaked with 5 show two anomalous signals, one of which is adjacent to the iodide binding site. The major conformation of 5 binding is shown (salmon), with placement inferred from anomalous density (Extended Data Fig. 6). Although the approach of 1 from ‘above’ the plane of 5 would be occluded by the protein scaffold, a putative nucleophile binding pocket could allow for approach from ‘below’. Solvent-accessible surface shown in transparent grey. Anomalous map contoured at 9σ (grey mesh). c, Comparison of residues in SNAr1.3 (blue) and BH32.7 (orange; PDB: 7O1D), which is the closest available structure to SNAr1.0 and contains a single Y20A mutation remote from the catalytic site, shows how evolution has modulated polar interactions in the halide binding cavity. d, Representative structure from molecular dynamics simulations places 1 in the putative nucleophile binding pocket and suggests that H-bonding interactions between Arg124 and the enolate of 1 may help to position the nucleophile for selective catalysis. A water molecule is shown as a red sphere.
