Table 3.
Hydrogen bond interactions between quinones in the QA and QB sites and the surrounding protein. Specific interactions are labeled according to the quinone atom using IUPAC nomenclature (Fig. 2). The atom on the protein residue that participates in the hydrogen bond is also specified. The percentage of time during the simulations when the hydrogen bond was formed, defined to exist when the donor and acceptor heavy atoms are within 3.2 Å and the hydrogen is within 30° of the line between them, are reported. Note that 2MeO-Q and 3MeO-Q have blank entries in the QB site that correspond to the hydrogen bonds that are missing due to the absence of the appropriate hydrogen bond acceptor atom (O2 in the case of 3MeO-Q and O3 in the case of 2MeO-Q). In these cases, the interaction distance is calculated to the methyl carbon that replaces the methoxy oxygen. Animations of the quinones in the QA and QB sites are provided as Supporting Information.
| Q-site:atom | RC-residue:atom | Hydrogen Bond Probability | Average Interaction Distance (Å) | ||||
|---|---|---|---|---|---|---|---|
| UbiQ | 2MeO-Q | 3MeO-Q | UbiQ | 2MeO-Q | 3MeO-Q | ||
| QA:O1 | AlaM260:N | 60.36 | 36.36 | 79.77 | 2.91 ± 0.00 | 3.15 ± 0.05 | 2.89 ± 0.01 |
| QA:O4 | HisM219:ND1 | 59.53 | 80.98 | 64.93 | 3.11 ± 0.02 | 2.92 ± 0.01 | 3.06 ± 0.01 |
|
| |||||||
| QB:O1 | IleL224:N | 61.90 | 39.45 | 51.37 | 2.97 ± 0.01 | 3.06 ± 0.02 | 3.07 ± 0.03 |
| QB:O2 | GlyL225:N | 17.66 | 4.73 | –– | 3.31 ± 0.04 | 3.27 ± 0.01 | 3.72 ± 0.04 |
| QB:O3 | HisL190:ND1 | 0.34 | –– | 3.93 | 4.28 ± 0.03 | 4.50 ± 0.02 | 4.25 ± 0.12 |
| QB:O4 | HisL190:ND1 | 38.37 | 75.08 | 23.19 | 3.07 ± 0.03 | 2.89 ± 0.01 | 3.23 ± 0.06 |