Figure 2.

Schematic views of D2.3 Fab residues that interact with the ligands examined. Residue numbering is according to ref. 24. In A–C, the ligands are in blue, the C_α trace of the Fab is in green, and water molecules are in red. Hydrogen bonds are shown as dotted lines. (A) Complex of D2.3 with amide 4, a stable SA. (B) Complex of D2.3 with TSA 3. (C) Complex of D2.3 with the reaction product 2, p-nitrobenzyl alcohol. Electron density corresponding to an acetate molecule was located in the combing site. The acetate is in yellow; the oxygens and the methyl of the acetate were distinguished on the basis of the hydrogen bonds established. A–C were drawn with molscript (25). (D) View of the canal (D2.3-4 structure) that allows water diffusion to the carbon atom of the carbonyl of 4 analogous to the reaction center in the complex of D2.3 with 1. The surface accessible to the exterior of a water molecule represented by a 1.4-Å radius sphere is cut to show the canal; its face toward the complexed Fab atoms is in blue, and the one facing the exterior is in white. Only the residues that border the canal are represented. Ligand 4 is in green; the water molecule (magenta) closest to the analogue of the reaction center is within hydrogen bonding distance and angle to Arg-H50 (hydrogen bond not shown). Nitrogen Nδ1 of His-H35 makes a hydrogen bond to Trp-H47 (not shown) that is conserved in antibodies; therefore, the Nɛ2 nitrogen of His-H35 (which is part of the canal’s wall) is protonated, and His-H35 most likely does not function as a general base in the hydrolysis catalyzed by D2.3. D was rendered in the avs environment (26).