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Figure 3.
FIGURE 3. Critical interactions between SCV RBD (green) and
Fab m396 (yellow and cyan for heavy- and light-chain CDRs,
respectively) depicted with 2F[o] – F[c] electron density maps
contoured at the 1.0  level. CDRs H1, H2, and
H3 recognize the major neutralizing site, the  6– 7 loop.
L3 exclusively contacts minor binding sites with the involvement
of bridging water molecules. a, H1 residues Ser-31 and Thr-33
form hydrogen bonds with RBD residues Thr-486 and Thr-488 via
backbone-side chain interactions. b, H2 displays a concave
surface and contributes to the specific interactions between H2
residues Thr-52 and Asn-58, and RBD residue Tyr-491. c, H3
residue Val-97 contacts the RBD and buries the largest surface
area per residue (108 Å^2) among all residues of the
antibody combining site. The carbonyl of Val-97 forms a hydrogen
bond to the side-chain amide of Gln-492 of RBD. d, L3 is the
only light chain CDR that binds to the RBD with two bridging
water molecules (pink spheres) involved.
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