Table 3. Quaternary-structure comparisons between PDB entry 4xs0 and reference Hbs.
| Hb structure† | PDB code | α1β1 r.m.s.d. (Å), all atom pairs (Cα atom pairs)‡ | α2β2 r.m.s.d (Å), all atom pairs (Cα atom pairs)‡ | Rotation§ (°) | Translation§ (Å) |
|---|---|---|---|---|---|
| T state | 2dn2 | 1.7 (1.0) | 4.1 (3.9) | 9.2 | 0.7 |
| R state | 2dn1 | 1.9 (1.1) | 7.4 (7.2) | 17.0 | 4.2 |
| R2 state | 1bbb | 2.3 (1.4) | 11.5 (11.4) | 27.9 | 6.0 |
| RR2 state | 1mko | 2.1 (1.4) | 9.7 (9.5) | 22.1 | 6.2 |
| R3 state | 1yzi | 1.9 (1.3) | 9.0 (8.9) | 20.1 | 4.4 |
| Human ζ2β2 S | 3w4u | 1.5 (1.0) | 1.8 (1.4) | 3.5 | 0.6 |
| Cat α2β2 | 3gqp | 1.5 (1.0) | 1.5 (1.0) | 1.1 | 0.1 |
†
The T-state and R-state reference structures are human deoxy-Hb and HbCO from Park et al. (2006 ▸), respectively, the R2 structure is from Silva et al. (1992 ▸), the RR2 and R3 structures are from Safo & Abraham (2005 ▸), the human variant Hb comprising ζHb and βS (carrying the sickle-cell mutation) is from Safo et al. (2013 ▸) and the low-affinity Hb from F. silvestris catus is from Balasubramanian et al. (2014 ▸).
‡
Comparison with the 4xs0 structure after superposing α1β1 dimers using residues of the BGH frame.
§
Rotation/translation needed to align α2β2 of the test structure with α2β2 of the 4xs0 structure after first superposing the α1β1 dimers according to the BGH frame.