Table 6.
Significant Carbohydrate-Protein hydrogen bond occupancies and Carbohydrate-H2O-Protein, Carbohydrate-H2O-Carbohydrate bridge water occupancies detected from MD simulation of the 3GLY crystal structure. Also presented are the distances between the heavy atoms involved in the hydrogen bond and bridge-water interactions from the crystal structure.
| Carbohydrate-Protein | |||
|---|---|---|---|
| Carbohydrate | Protein | Occupancy | dA-B (crys)a |
| Man-8 (HO2) | Ala-86 (O) | 0.826 | 2.62 |
| Man-4 (HO4) | Gly-456 (O) | 0.513 | 4.34 |
| Man-9 (HO2) | Ser-460 (O) | 0.473 | 2.88 |
| Man-3 (HO2) | Gln-168 (O) | 0.231 | 5.05 |
| Man-2 (HO4) | Val-445 (O) | 0.195 | 4.77 |
|
| |||
| Carbohydrate-H2O-Proetin | |||
|
| |||
| 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 |
|
| |||
| Carbohydrate-H2O-Carbohydrate | |||
|
| |||
| Carbohydrate | Carbohydrate | Occupancy | dA-H2O,dB-H2O (crys) a |
|
| |||
| Man-9 (O3/HO3) | Man-8 (O4/HO4) | 0.323 | 2.82,2.73 |
| Man-9 (O2/HO2) | Man-7 (O3/HO3) | 0.261 | 3.11,4.00 |
| Man-6 (O2/HO2) | Man-4 (O6/HO6) | 0.169 | --- |
a
all distances are in Å.