Table 2.
Summary of glycosidic angle (χ)a of the guanine residues in VR-loops consisting of natural DNA nucleotides
| PDB code | Measured χ value (°) for 5′-dG | Measured χ value (°) for 3′-dG | Reference |
|---|---|---|---|
| 1U64 | 75.2 ± 6.1 (syn) | 319.4 ± 0.9 (undefined) | (72) |
| 2KPR | 40.6 ± 5.6 (syn) | 313.9 ± 12.7 (undefined) | (85) |
| 6H1K | 72.2 ± 25.6 (syn) | 333.3 ± 11.5 (undefined)b | (45) |
| 5ZEV | 77.1 ± 1.2 (syn) | 275.1 ± 1.1 (undefined) | (81) |
| 6A7Y | 64.8 ± 5.0 (syn) | 343.7 ± 6.9 (undefined) | (82) |
| 5O4D | 87.2 ± 2.4 (syn) | 274.2 ± 6.8 (undefined) | (84) |
| 6KVB | 72.3 ± 25.7 (syn) | 317.0 ± 6.2 (undefined) | This work |
| 6JCD | 155.4 ± 6.2 (undefined) | 64.2 ± 3.1 (syn) | (71) |
aThe ranges for anti and syn glycosidic angles (χ) are defined as 240° > χ > 180° and 0 < χ < 90° respectively (86). Glycosidic angles outside of these ranges are marked as undefined.
bThe glycosidic angle extracted from the solution structure (PDB code, 6H1K) falls in the undefined range, although the reference described it as a syn conformation.