Table 7.
Curvature data for bound DNA duplexes of length ≥ 18 basepairs, excluding terminal basepairs, for the HTH-bound DNA dataset.
| PDB ID | LENGTH | Succ. Bend. Ang. (°) | End-to-end (°) Bend. Ang. | d/llocal | R.O.C.(Å) | RMSD (Å) | Geometry Assigned | Out-of-Plane (°) Bend. Ang. | |||||
| AVG. | S.D. | MAX. | Cfit | Lfit | Cfit/Lfit | ||||||||
| Value | Position | ||||||||||||
| 1KX5 | 30 | 15.1 | 10.5 | 51.9 | A10A11A12 | 126.7 | 0.77 | 37.9 | 0.6 | 20.0 | 0.03 | C | 0.1 |
| 1J59 | 28 | 25.3 | 16.2 | 66.5 | T9G10A11 | 98.5 | 0.85 | 47.2 | 0.7 | 21.4 | 0.03 | C | -41.9 |
| 1RUN | 28 | 30.4 | 17.1 | 71.1 | T9G10A11 | 109.7 | 0.85 | 47.8 | 0.6 | 22.2 | 0.03 | C | -50.6 |
| 1CGP | 26 | 19.1 | 18.9 | 65.9 | G7T8G9 | 72.4 | 0.86 | 48.2 | 0.8 | 17.9 | 0.04 | C | -51.1 |
| 1BL0 | 20 | 10.5 | 6.1 | 25.0 | A6G7C8 | 38.8 | 0.94 | 47.0 | 0.7 | 3.6 | 0.19 | C | -68.9 |
| 1HLV | 19 | 10.0 | 7.6 | 30.1 | G15G16G17 | 39.3 | 0.95 | 54.6 | 0.6 | 3.3 | 0.18 | C | -129.0 |
| 1APL | 18 | 11.8 | 7.3 | 33.0 | A16C17G18 | 3.7 | 0.99 | NA | 4.9 | 0.9 | 5.44 | L | NA |
| 1K78 | 23 | 9.1 | 3.2 | 15.6 | T19G20G21 | 15.9 | 1.00 | NA | 2.4 | 1.0 | 2.40 | L | NA |
| 4CRX | 32 | 11.8 | 12.2 | 56.5 | A17T18G19 | 76.3 | 0.82 | NA | 3.4 | 9.1 | 0.37 | U | NA |
| 1GDT | 32 | 15.4 | 13.0 | 60.3 | T14T15A16 | 40.2 | 0.87 | NA | 1.6 | 14.5 | 0.11 | U | NA |
| 1MNM | 23 | 11.8 | 7.8 | 26.8 | G13A14A15 | 58.7 | 0.89 | NA | 1.7 | 5.4 | 0.31 | U | NA |
| 1JE8 | 18 | 23.0 | 13.0 | 49.6 | T2A3C4 | 56.9 | 0.93 | NA | 1.1 | 5.0 | 0.22 | U | NA |
| 1DDN | 23 | 8.8 | 4.4 | 19.1 | T13T14A15 | 36.0 | 0.95 | NA | 7.7 | 2.5 | 3.08 | U | NA |
| 1L3L | 18 | 9.0 | 5.9 | 19.7 | C14A15C16 | 32.5 | 0.96 | NA | 1.5 | 1.6 | 0.94 | U | NA |
| 1U78 | 23 | 10.6 | 12.3 | 51.1 | T10A11G12 | 41.3 | 0.97 | NA | 1.4 | 19.6 | 0.07 | U | NA |
| 1Z9C | 24 | 10.0 | 5.9 | 23.9 | T11A12T13 | 3.4 | 0.97 | NA | 6.1 | 2.0 | 3.05 | U | NA |
| 1H88 | 23 | 7.4 | 4.5 | 16.8 | C8A9A10 | 12.3 | 0.98 | NA | 1.6 | 7.8 | 0.21 | U | NA |
| 1D5Y | 18 | 8.9 | 5.7 | 21.6 | C15A16A17 | 10.6 | 0.98 | NA | 2.6 | 2.0 | 1.30 | U | NA |
| 1K61 | 18 | 8.8 | 6.1 | 22.3 | T4A5A6 | 6.6 | 0.99 | NA | 1.3 | 7.1 | 0.18 | U | NA |
| 1DU0 | 18 | 6.3 | 4.0 | 15.2 | C15C16T17 | 10.1 | 0.99 | NA | 0.6 | 2.9 | 0.21 | U | NA |
| 1RIO | 25 | 14.8 | 8.7 | 34.1 | C8C9G10 | 16.1 | 0.99 | NA | 0.6 | 2.7 | 0.22 | U | NA |
| 6PAX | 22 | 11.8 | 7.1 | 25.6 | A8C9G10 | 20.4 | 0.99 | NA | 0.6 | 2.1 | 0.29 | U | NA |
| 2HDD | 18 | 10.7 | 5.4 | 23.3 | T12C13C14 | 22.9 | 0.99 | NA | 1.2 | 1.8 | 0.67 | U | NA |
| 1HDD | 18 | 10.9 | 4.1 | 19.9 | G3C4C5 | 1.9 | 0.99 | NA | 2.6 | 1.4 | 1.86 | U | NA |
| 3HDD | 18 | 6.5 | 3.7 | 14.4 | G8T9A10 | 8.3 | 0.99 | NA | 3.0 | 1.4 | 2.14 | U | NA |
| 1JT0 | 26 | 10.4 | 5.9 | 22.1 | A23T24A25 | 29.8 | 0.99 | NA | 9.1 | 1.1 | 8.27 | U | NA |
| 1F4K | 19 | 7.9 | 5.1 | 20.2 | T3G4A5 | 24.8 | 1.00 | NA | 0.8 | 2.4 | 0.33 | U | NA |
| 1MDM | 23 | 9.2 | 4.7 | 20.8 | A6G7A8 | 15.6 | 1.00 | NA | 1.7 | 1.1 | 1.55 | U | NA |
| 1HF0 | 20 | 10.5 | 7.3 | 30.7 | T6G7A8 | 28.6 | 1.01 | NA | 1.4 | 0.9 | 1.56 | U | NA |
The calculation of successive bending angles, end-to-end bending angle, d/llocal, Radius of Curvature (ROC), RMSD for circle fit (Cfit) and line fit (Lfit) and torsion angle for out-of-plane component of bending have been described in the 'Methods' section. 'MAX.' denotes the position and value of the maximum successive bending angle within the particular structure. The criteria used to assign DNA molecule geometry as curved (C), linear (L) or unassigned (U) have also been described in the 'Methods' section. The radius of curvature (ROC) and out-of-plane component of bending are reported only when a DNA molecule's geometry is assigned as curved.