Table 2.
Hydrogen bond occupancies for simulations of different protonation states. See Table 1 and Figure 1 for the protonation states in the different simulations.
| Simulation | Acceptora | Donora | Occupancyb,c |
|---|---|---|---|
| A | O2A(PRAa3) | OD2(Asp372) | 58.8% |
| O1A(PRAa3) | OD2(Asp372) | 36.2% | |
| O(Asp372) | N(ε-His376) | 4.7% | |
| B | OD2(Asp372) | O2A(PRAa3) | 95.4% |
| OD1(Asp372) | O2A(PRAa3) | 12.0% | |
| O(Asp372) | N(ε-His376) | 51.6% | |
| C | O1A(PRAa3) | OD2(Asp372H) | 68.6% |
| OD1(Asp372H) | O2A(PRAa3) | 9.1% | |
| ND1(ε-His376) | O2A(PRAa3) | 50.5% | |
| O(Asp372H) | N(ε-His376) | 79.2% | |
| OE1(Glu126II) | NE2(ε-His376) | 8.8% | |
| OE2(Glu126II) | NE2(ε-His376) | 7.5% | |
| D | O1A(PRAa3) | OD2(Asp372H) | 99.6% |
| O1A(PRAa3) | ND1(His376H+) | 90.6% | |
| O2A(PRAa3) | ND1(His376H+) | 46.6% | |
| O(Asp372H) | N(His376H+) | 58.8% | |
| OE1(Glu126II) | NE2(His376H+) | 51.4% | |
| OE2(Glu126II) | NE2(His376H+) | 44.3% | |
| E | NE2(δ-His376) | OE2(Glu126HII+) | 29.8% |
| O1A(PRAa3) | OD2(Asp372H) | 46.0% | |
| O2A(PRAa3) | OD2(Asp372H) | 25.2% | |
| O1A(PRAa3) | ND1(δ-His376) | 61.3% | |
| O2A(PRAa3) | ND1(δ-His376) | 46.6% | |
| O(Asp372H) | N(δ-His376) | 82.2% |
a:
Names and residue name of the heavy atoms involved in the hydrogen bond, with the residue name in parentheses. Residues PRAa3, Asp372, His376 and Glu126II are considered.
b:
Only occupancies larger than 3% are listed.
c:
Occupancy is the fraction of simulation frames during which the hydrogen bond is present. Hydrogen bonds are defined through an angle cutoff of 135° and a distance cutoff of 3.0 Å between the hydrogen bonded atoms.