Table 2.
Torsion angles relating atoms C6–C5–C5A–O5 of the 5hmC bases in cross-over and continuous strands in the current junction structure, and in B-DNA duplexes from the literature. A torsion angle of 0° indicates the hydroxyl is in plane with the base and pointed towards the glycosidic bond, while a 180° angle points the hydroxyl towards the N4 amine group. Positive angles place the hydroxyl above the plane of the base in the 5′ direction and negative angles are in the 3′ direction.
| Junction DNA (PDB 5DSB) | |
|
| |
| Crossover Strand (R1) | −12.0° |
| Crossover Strand (R2) | 111.4° |
| Continuous Strand | 92.3° |
|
| |
| Published out of plane rotamers | |
|
| |
| 4HLIa | 132.8° |
| 4GLCa | 126.9° |
| 4GLCa | 96.1° |
| 4GLHa | 115.7° |
| 4GLHa | 109.8° |
| 4I9Vb | 111.0° |
| 4I9Vb | 112.1° |
| Average (Standard Deviation) | 114.9° (12.0°) |
|
| |
| Published rotamer outliers | |
|
| |
| 4HLIa | 72.6° |
| 4I9Vb | 24.7° |
a
Renciuk, D. et al. Nucleic Acids Res. 2013
b
Szulik, M.W. et al., Biochemistry 2015