TABLE 3.
Comparison of the interactions between carbohydrate ligands and Stx1 (PDB code 1BOS) and Stx2a (this report)
| Stx1-PkMCO | Stx2a-2 | |
|---|---|---|
| Site 1 | ||
| H-Bonds | Gal1NAc:O7-N:Glu-15 (2.7, 2.9)a | |
| Gal1NAc:O7-Nζ:Lys-12 (3.4) | ||
| Gal1NAc:O3-Nζ:Lys-12 (2.9) | ||
| Gal1NAc:O4-Oϵ1:Glu-27 (2.7, 2.6) | ||
| Gal1NAc:O4-Oγ1:Thr-20 (2.9) | ||
| Gal1NAc:O6-Oϵ1:Glu-27 (2.9) | ||
| Gal1:O5-Oγ1:Thr-21 (3.2)b | Gal1NAc:O5-Oγ1:Thr-20 (3.1) | |
| Gal2:O6-Oδ2:Asp-17 (2.5) | Gal2:O6-Oδ2:Asp-16 (2.6) | |
| Gal2:O3-O:Gly-60 (2.6) | Gal2:O3-O:Gly-59 (2.8) | |
| VDWc | 37 | 51 |
| Site 2 | ||
| H-bonds | Gal1:O2-Oδ1:Asp-16 (2.8) | Gal1NAc:O7-Nη2:Arg-32 (3.1) |
| Gal1:O3-Nη2:Arg-33 (2.8) | Gal1NAc:O3-Nη2:Arg-32 (3.2) | |
| Gal1:O4-Oδ1:Asn-32 (2.7) | Gal1NAc:O4-Oγ:Ser-31 (3.2) | |
| Gal1:O4-Nϵ:Arg-33 (3.0) | Gal1NAc:O4-Nϵ:Arg-32 (3.0) | |
| Gal1:O4-Nη2:Arg-33 (3.5) | Gal1NAc:O4-Nη2:Arg-32 (3.3) | |
| Gal1:O6-Oδ1:Asn-32 (3.0) | Gal1NAc:O6-Oγ:Ser-31 (3.3) | |
| Gal1:O6-N:Asn-32 (3.1) | Gal1NAc:O6-N:Ser-31 (2.9) | |
| Gal1:O6-O:Phe-63 (2.9) | Gal1NAc:O6-O:Phe-62 (2.7) | |
| Gal2:O2-N:Gly-61 (3.2, 2.9)d | ||
| Gal2:O3-N:Gly-61 (3.0, 2.9)d | ||
| Gal2:O5-Oγ:Ser-54 (3.2) | ||
| Gal2:O6-Oγ:Ser-54 (2.8) | ||
| Gal2:O6-N:Asn-55 (3.2) | Gal2:O6-N:Ser-54 (2.9) | |
| Gal2:O6-Oϵ2:Glu-15 (3.3) | ||
| VDW | 46 | 59 |
a Solvent-bridged interaction between the ligand and the toxin (the H-bond distance between residue 1 and water, the H-bond distance between residue 2 and water).
b Distance in Å between the two atoms forming the hydrogen bond.
c VDW, number of van der Waals contacts between the ligand and the toxin.
d These solvent-bridged interactions were also observed in Stx1-starfish complex (PDB code 1QNU).