Occurrence and volume statistics of pockets depicted in Fig. 7 in MD simulations and available PDB structures. The rows in the experimental structures represent the different chains. Note that the minimum volume for any pocket to be defined is 200 Å3.
| Force field | ATP pocket | RNA pocket | RecA2 pocket1 | RecA2 pocket2 | RecA2 pocket3 | Stalk pocket | ZBD pocket | ||
|---|---|---|---|---|---|---|---|---|---|
| (%) | Holo | CHARMM | 96.28 | 98.60 | 18.45 | 22.25 | 54.57 | 26.52 | 16.91 |
| Amber | 98.28 | 98.18 | 34.92 | 18.12 | — | 16.40 | 20.26 | ||
| Apo | Amber | 81.40 | 99.74 | 35.06 | — | 37.00 | 17.77 | 7.89 | |
| Volume (stdev)/Å3 | Holo | CHARMM | 630 (263) | 1472 (858) | 276 (64) | 409 (179) | 405 (200) | 449 (202) | 268 (74) |
| Amber | 542 (223) | 1911 (565) | 330 (91) | 353 (119) | — | 300 (75) | 246 (47) | ||
| Apo | Amber | 665 (338) | 2415 (873) | 303 (106) | — | 286 (99) | 282 (73) | 247 (50) | |
| 6jyt | X-ray | 4058 | 334 | 204 | — | — | — | ||
| 4427 | 1282a | — | 1282a | — | — | ||||
| 6zsl | 474 + 267b | — | — | — | — | — | — | ||
| 613 | — | — | — | — | — | — | |||
| 6xez | Cryo-EM | 534 | 3698 | 662 | — | — | 279 | — | |
| 4891 | 540 | — | — | — | — | ||||
| 7cxm | 708 | 2780 | 588 | 369 | — | — | — | ||
| 782 | 1566 | — | — | — | — | — | |||
a
Labelled pockets are connected, the combined volume is shown.
b
Made of two separate pockets.