Table I.
Key interactions between the 6′-SLN and PSL residues from the X-ray structure and MD simulation
| Interatomic distancea |
||
|---|---|---|
| X-ray | MD (10 ns) | |
| Direct H-bonds | ||
| Neu5Ac(O1A)·Ser32(Oγ) | 2.56 | 2.64 ± 0.12 (100%)b |
| Neu5Ac(O1A)·Ser32(N) | 3.07 | 3.22 ± 0.25 (87%) |
| Neu5Ac(O8)·Ser32(N) | 3.33 | 3.15 ± 0.21 (94%) |
| Neu5Ac(N5)·Asn30(O) | 2.59 | 3.00 ± 0.24 (96%) |
| Gal(O3)·Asp72(Oδ2) | 2.67 | 2.60 ± 0.09 (100%) |
| Gal(O4)·Asp72(Oδ1) | 2.64 | 2.59 ± 0.14 (100%) |
| Gal(O2)·His76(Nε2) | 2.60 | 2.86 ± 0.08 (99%) |
| Gal(O3)·Asn94(Nδ2) | 2.94 | 2.93 ± 0.16 (100%) |
| Aromatic stacking interactionsc | ||
| rGal·Tyr87 | 4.46 | 4.45 ± 0.01 |
| θGal·Tyr87 | 157.64 | 158.4 ± 4.90 |
aValues are expressed in Å. The electron density for chain A was the better ordered among the two NCS-related protomers; therefore, representative H-bond distances were calculated using this protomer.
bFor the MD data, the distances were averaged over 10 ns and H-bond length (±1 SD) and occupancy assessed for periods during which the distance between the heavy atoms was < 3.5 Å.
cDistance (r) in Å between the centroid (c) of the galactosyl ring and the tyrosine phenyl ring, and angle (θ) between the normal to the tyrosine ring plane and the vector between the centroid c, in degrees (Ford et al. 2003).