Figure 2.
Fig. 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[ ]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 N 1 of
His-H35 makes a hydrogen bond to Trp-H47 (not shown) that is
conserved in antibodies; therefore, the N 2 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).
]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 N 
1 of
His-H35 makes a hydrogen bond to Trp-H47 (not shown) that is
conserved in antibodies; therefore, the N 
2 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).