Table 1.
Significant Carbohydrate-H2O-Protein bridge water occupancies occurring in the 3GLY MD simulation. Also presented are the distances between the heavy atoms involved in the bridge-water interactions from the crystal structure.
| O-linkages
| |||
|---|---|---|---|
| Carbohydrate-H2O-Protein
| |||
| Carbohydrate | Protein | Occupancy | dA-H2O, dB-H2O (crys)a |
|
| |||
| Man-8 (O3/HO3) | Val-461 (O) | 0.710 | 2.84, 2.66 |
| Man-4 (O3/HO3) | Tyr-458 (HN) | 0.608 | 2.71, 3.09 |
| Man-6 (O2/HO2) | Ser-455 (O) | 0.431 | --- |
| Man-4 (O2/HO2) | Ser-99 (O) | 0.378 | 3.34, 2.50 |
| Man-8 (O2/HO2) | Ile-87 (O) | 0.279 | 2.81, 3.15 |
| N-linkages
| |||
|---|---|---|---|
| Carbohydrate-H2O-Protein
| |||
| Carbohydrate | Protein | Occupancy | dA-H2O, dB-H2O (crys)a |
|
| |||
| Asn-171 | |||
|
| |||
| β-GlcNAc-1 (O6/HO6) | Gln-219 (O) | 0.803 | 2.48, 2.97 |
| β-GlcNAc-1 (O) | Ser-184 (O/OH) | 0.776 | 2.58, 2.65 |
| β-GlcNAc-1 (O6/HO6) | Ser-226 (O) | 0.775 | 2.85, 3.75 |
| β-GlcNAc-1 (O6/HO6) | Ala-450 (O) | 0.655 | 2.48, 2.96 |
| β-GlcNAc-1 (O3/HO3) | Tyr-223 (O/OH) | 0.565 | 2.87, 2.89 |
| β-GlcNAc-1 (O) | Trp-170 (O) | 0.525 | 2.58, 2.81 |
| β-GlcNAc-2 (O6/HO6) | Asp-238 (Oδ1/Oδ2) | 0.513 | 3.08, 4.16 |
| Man-5 (O2/HO2) | Arg-241 (O) | 0.354 | 4.17, 2.63 |
| Man-5 (O3/HO3) | Arg-241 (O) | 0.216 | 3.51, 2.63 |
|
| |||
| Asn-395 | |||
|
| |||
| Man-7 (O3/HO3) | Ser-399 (O/OH) | 0.876 | 2.63,2.81 |
| Man-7 (O3/HO3) | Ser-411 (O) | 0.805 | 2.63,2.79 |
| β-GlcNAc-1 (O6/HO6) | Asn-395 (O) | 0.629 | --- |
| β-GlcNAc-1 (O) | Asp-414 (Oδ1/Oδ2) | 0.922 | --- |
| Man-7 (O4/HO4) | Arg-413 (NH2) | 0.500 | 3.11,3.22 |
| Man-7 (O4/HO4) | Thr-43 (O/OH) | 0.493 | 3.11,2.89 |
| Man-3 (O6/HO6) | Trp-28 (O) | 0.494 | 2.66,2.52 |
| Man-2 (O6/HO6) | Trp-28 (O) | 0.454 | 2.84,2.52 |
a
all distances are in Å.