Crystal structures of AMP and BocLys-AMP bound to PylRS. (a, b) The Fo − Fc OMIT electron-density maps (contoured at 4σ) of the bound AMP (PDB entry 3vqx
, molecule A) (a) and BocLys-AMP (PDB entry 3vqx
, molecule C) (b) are represented as ball-and-stick models. Transparent ribbon models of the AMP-bound (and BocLys-AMP-bound) forms are visible in the background. (c) Superposition of the structures of the previously determined form 1 (white) and BocLys-AMP-bound (grass green) forms. (d) Superposition of the structures of the Pyl-AMP-bound (white) and BocLys-AMP-bound forms (grass green). (e) The Asn346 side chain hydrogen-bonds to the carbonyl group of the amino-acid substrate and a water-mediated hydrogen bond exists between the α-carboxyl group of BocLys (or the α-amino group of pyrrolysyl-AMP) and the side-chain amide group of Asn346.