Table II.
Comparison of Computed and Crystallographic Geometrical Parameters for RnQSOX1
| Conf. 1 | Conf. 2 | Free MD | X-ray molecule A | X-ray molecule B1 | X-ray molecule B2 | |
|---|---|---|---|---|---|---|
| SγC73 − SγC76 (Å) | 3.64 ± 0.43 | 3.81 ± 0.40 | 3.48 ± 0.38 | 2.03 | 2.02 | 3.57 |
| SγC452 − SγC455 (Å) | 2.19 ± 0.08 | 2.94 ± 0.10 | 3.49 ± 0.39 | 2.03 | 2.03 | 4.16 |
| SγC73 − SγC452 (Å) | 2.80 ± 0.08 | 2.14 ± 0.06 | 2.08 ± 0.05 | 3.68 | 3.70 | 2.03 |
| SγC73 − SγC452 − SγC455 (°) | 156.5 ± 5.5 | 152.6 ± 6.5 | 151.4 ± 6.6 | 143.4 | 125.0 | 119.5 |
| χ1C73 (°) | 170.2 ± 8.5 | 174.8 ± 7.5 | 173.9 ± 7.6 | 155.1 | 165.2 | −174.2 |
| χ1C76 (°) | −52.3 ± 8.8 | −55.1 ± 8.0 | −53.5 ± 8.0 | −51.0 | −43.20 | −89.5 |
| χ1C452 (°) | −171.1 ± 6.1 | −161.0 ± 6.9 | −159.5 ± 7.6 | −174.2 | 179.2 | −58.5 |
| χ1C455 (°) | −54.1 ± 6.0 | −59.5 ± 6.2 | −62.7 ± 7.5 | −52.5 | −52.1 | −55.8 |
| SγC455 − N5FAD (Å) | 3.59 ± 0.23 | 3.32 ± 0.12 | 3.24 ± 0.11 | 3.92 | 3.95 | 3.82 |
The computed geometrical parameters were obtained as an average over 520 MD configurations each. Values in columns “Conf. 1” and “Conf. 2” were obtained from trajectories based on PMF simulations in the reactant and product wells, with intra- and interdomain disulfide bridges, correspondingly. Values in column “Free MD” were obtained from free MD simulations without restraints, which correspond to the interdomain disulfide conformation. For the geometrical parameters obtained from the X-ray crystal structures, molecule A and the first modeled conformation of molecule B (B1) contain the disulfide bonds C73–C76 and C452–C455. The second modeled conformation of molecule B (B2) contains the interdomain disulfide C73–C452.