Table 1. Reannotations to Mg2+ ions that have been made for densities in the vicinity of N7, O6 or O4 atoms (bold) of guanosines, adenines or uridines, respectively (28S rRNA; no changes in 18S rRNA).
The observed coordination is often octahedral, which is typical of Mg2+, but it cannot be excluded that some positions are other ions (K+ is present in the buffer, but coordination around K+ is less regular, often with more than six ligands with longer coordination distances) or water molecules. The coordinates of the human ribosome structure in the PDB were updated accordingly. Human 28S rRNA sequence, NR_003287.2; human 80S ribosome, PDB entry 6ek0; human 80S ribosome, EMBD entry EMD-3883.
| 28S rRNA residue name | Previous annotation | Comments |
|---|---|---|
| G237 | xp6G237 | Mg2+ (distance between O6 and Mg2+ ion is 2.6 Å) |
| U1348 | xp4U1348 | Mg2+ (distance between O4 and Mg2+ ion is 2.3 Å); see also calculated ESP map (Fig. 1 ▸) |
| G1574 | xp6G1574 | Mg2+ (distance between O6 and Mg2+ ion is 2.2 Å) |
| G1605 | m7G1605 | Weak Mg2+ (distance between N7 and Mg2+ ion is 2.0 Å) |
| U1659 | xp4U1659 | Mg2+ (distance between O4 and Mg2+ ion is 2.1 Å) |
| G1797 | xe7G1797 | Mg2+ (distance between N7 and Mg2+ ion is 2.2 Å) |
| G1909 | xp7G1909 | Mg2+ (distance between N7 and Mg2+ ion 2.9 Å) |
| G2297 | xe7G2297 | Mg2+ (distance between N7 and Mg2+ ion 2.8 Å) |
| G2380 | m6G2380 | Weak Mg2+ (distance between O6 and Mg2+ ion is 1.6 Å) |
| G2522 | m7G2522 | Mg2+ (distance between N7 and Mg2+ ion is 2.8 Å) |
| G2754 | xp6G2754 | Mg2+ (distance between O6 and Mg2+ ion is 2.1 Å) |
| G3880 | xp7G3880 | Mg2+ (distance between N7 and Mg2+ ion is 2.7 Å) |
| G3897 | ac7G3897 | Mg2+ (distance between N7 and Mg2+ ion is 2.4 Å); see also calculated ESP map (Fig. 1 ▸) |
| Gm3899 | ac7Gm3899 | Mg2+ at N7 (distance between N7 and Mg2+ ion is 2.2 Å) |
| G4129 | m6G4129 | Weak Mg2+ (distance between O6 and Mg2+ ion is 1.8 Å) |
| G4185 | m6G4185 | Weak Mg2+ (distance between O6 and Mg2+ ion is 2.2 Å) |
| U4194 | xp4U4194 | Mg2+ (distance between O4 and Mg2+ ion is 2.2 Å) |
| G4355 | xe6G4355 | Mg2+ (distance between O6 and Mg2+ ion is 2.2 Å) |
| G4371 | m2xp7G4371 | Mg2+ (distance between N2 and Mg2+ ion is 2.4 Å) |
| G4472 | m6G4472 | Mg2+ (distance between O6 and Mg2+ ion is 2.1 Å) |
| m6G4529 | m6G4529 | Weak Mg2+ (distance between O6 and Mg2+ ion is 1.7 Å) |
| G4550 | m7G4550 | Mg2+ (distance between N7 and Mg2+ ion is 2.9 Å) |
| A4564 | m7A4564 | Possible Mg2+ or water molecule (distance to N7 is 1.5 Å) |
| G4690 | ac7G4690 | Mg2+ (distance between N7 and Mg2+ ion is 2.2 Å) |