Table 1.
Rigid-body parameters of G·A pairings in RNA structures*
| G·A pair | # † | Shear (Å) | Stretch (Å) |
Stagger (Å) |
Buckle (deg) |
Propeller (deg) |
Opening (deg) |
Vbp (Å3deg3) |
|
|---|---|---|---|---|---|---|---|---|---|
| m−m | 141 | −1.84±0.86 | 7.19±0.62 | 0.01±1.54 | −2.0±25.3 | −8.9±22.1 | 150.0±15.3 | 1116 | |
| m−W | 153 | 3.74±1.37 | 3.44±2.17 | 0.33±1.28 | −8.0±30.2 | −16.0±26.6 | 101.5±31.1 | 5851 | |
| m−WI | 125 | 3.14±0.57 | 4.39±0.79 | 0.17±1.31 | −3.4±29.9 | −16.6±27.5 | 113.1±20.6 | 1700 | |
| m−WII | 28 | 6.40±0.34 | −0.83±0.74 | 1.04±0.84 | −28.2±23.1 | −13.2±22.0 | 49.6±8.8 | 274 | |
| m−M | sheared | 1338 | 6.83±0.38 | −4.48±0.58 | 0.37±0.57 | 5.8±16.0 | −3.0±14.9 | −8.5±14.1 | 153 |
| m−MI | 1216 | 6.75±0.28 | −4.39±0.50 | 0.35±0.54 | 5.4±15.8 | −2.2±14.9 | −5.0±8.7 | 73 | |
| m−MII | 122 | 7.63±0.35 | −5.33±0.59 | 0.62±0.77 | 10.1±17.5 | −10.4±12.0 | −43.9±6.3 | 132 | |
| W−M | 59 | 7.10±1.52 | −2.84±2.36 | −0.08±1.13 | −1.5±25.4 | −4.0±23.7 | −69.6±24.5 | 14440 | |
| M−M | 25 | 0.37±2.52 | 4.49±0.86 | 0.11±1.66 | 7.0±25.0 | 5.5±19.5 | −154.1±25.5 | 1870 | |
| M−W | 16 | −4.24±0.74 | 0.89±1.23 | −02±0.98 | 6.5±20.7 | 0.3±15.3 | −93.4±28.6 | 386 | |
| W−m | 38 | −3.39±1.05 | 4.27±2.43 | 0.35±1.69 | 7.0±31.3 | −0.2±36.9 | 106.2±33.7 | 6687 | |
| W−W | imino | 344 | 0.07±0.72 | 1.55±0.42 | −0.33±0.55 | 6.7±15.2 | −9.6±16.8 | −16.4±14.0 | 465 |
| m+M | 53 | 6.42±1.09 | 0.29±2.79 | 0.38±1.39 | −15.5±24.3 | 11.4±23.9 | −3.3±29.2 | 15556 | |
| .+W | 27 | 2.35±0.48 | −4.94±0.73 | −0.34±1.47 | 5.1±34.3 | 8.2±18.8 | −125.2±12.0 | 206 | |
| m+W | 388 | 1.59±2.54 | −5.11±1.58 | −0.04±0.90 | −4.4±22.7 | 11.8±21.5 | −97.6±35.0 | 1762 | |
| m+WI | 267 | 3.23±0.72 | −4.12±0.64 | −0.12±0.82 | 0.1±22.1 | 14.0±24.5 | −77.2±19.9 | 553 | |
| m+WII | 121 | −2.02±0.64 | −7.30±0.35 | 0.15±1.04 | −13.8±21.2 | 6.7±11.5 | −142.6±10.0 | 54 | |
| m+. | 55 | −2.31±0.82 | −6.95±0.51 | 1.21±1.36 | −35.7±31.7 | 1.6±9.9 | −146.6±13.1 | 20 | |
| m+m | 395 | −2.70±0.35 | −7.38±0.33 | −0.08±1.42 | −11.1±29.5 | 8.7±18.3 | −153.8±9.8 | 111 | |
| W+M | 69 | 0.29±1.68 | 4.47±0.90 | 0.22±1.05 | −7.2±19.7 | 8.3±25.7 | −104.8±39.2 | 14442 | |
| .+M | 24 | 6.25±0.38 | 0.61±0.67 | −0.01±1.10 | −8.2±15.5 | 1.7±21.7 | −61.2±11.8 | 58 | |
| M+M | 26 | 0.19±6.06 | 1.08±5.39 | 0.17±0.94 | −12.2±26.4 | 5.4±18.0 | −30.2±142.0 | 56463 | |
| M+W | 29 | 0.58±1.70 | −4.8±1.20 | −0.29±0.92 | 5.5±22.1 | 4.3±16.4 | 102.2±20.2 | 1960 | |
*
Structures taken from the dataset of non-redundant, high-resolution RNA crystal structures curated by Leontis and Zirbel.59 Similar results are found with other datasets, e.g., the RNA09 coordinate files curated by the Richardson group at URL:http://kinemage.biochem.duke.edu/databases/rnadb.php.
†
Counts do not distinguish cis (c) and trans (t) arrangements of C1′–N9⋯N9–C1′angles reported by the software (Table S2) and used by others9,41 to distinguish pairing modes. This ‘chemical’ descriptor does not always match the ± directional criteria used here, e.g., the m−W states include a small number of t arrangements and the m+W states some c arrangements.