TABLE 6.
Observed hydrogen bonds (atomic distance <3.1 Å) between the ligand and the amino acids of DlADH during 650–750 ps of MD simulations
| TFE
|
PYR
|
|||
|---|---|---|---|---|
| Ionization scenario | Donor/acceptor | Occupancy (%) | Donor/acceptor | Occupancy (%) |
A: 
|
TFE/Tyr-151 | 100 | PYR-N1/Ser-138 | 90.4 |
| PYR-N1/Thr-140 | 64.6 | |||
| B: Ser-OH/Tyr-O−/Lys-NH2 | Ser-138/TFE | 19.8 | PYR-N1/Ser-138 | 52 |
| NAD-O2′/TFE | 25 | PYR-N1/Tyr-151 | 99.8 | |
| TFE/Tyr-151 | 100 | |||
| TFE /NAD-O2′ | 20.2 | |||
C:  †
|
NAD-O2′/TFE | 32.4 | Thr-140/PYR-N1 | 29.2 |
| Ser-138/TFE | 26.4 | Ser-138/PYR-N1 | 85.6 | |
| TFE/Tyr-151 | 100 | PYR-N1/Tyr-151 | 68 | |
| TFE/NAD-O2′ | 26.8 | |||
C:  ‡
|
NAD-O2′/TFE | 32 | Ser-394/PYR-N1 | 52.4 |
| Ser-394/TFE | 20.8 | PYR-N1/Ser-394 | 24.8 | |
| TFE/Tyr-407 | 100 | PYR-N1/Tyr-407 | 94 | |
| TFE/NAD-O2′ | 28.8 | |||
Hydrogen bonds observed in >20% of the sampled coordinate sets are included. Occupancy indicates the percentage of sampled coordinate sets with that particular hydrogen bond shorter than 3.1 Å.
†
subunit A of the dimer.
‡
subunit B of the dimer.