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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 4tp6



4TP6 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to virginiamycin m1. this file contains the 30s subunit of the second 70s ribosome.
List of all 39 Mg2+ binding sites in the PDB structure 4tp6 in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4tp6 A1604 Oph·Ob A:A195(OP2) U:A180(O4) A1714, A1715, A1716, A1717 A:A179, C:A194 A:A181, A:A179
4tp6 A1607 Oph·Ob G:A558(OP1) G:A299(O6) A1728, A1729, A1730, A1731 G:A297 A:A298, G:A566
4tp6 A1613 cis-2Oph A:A509(OP2), A:A510(OP2) A1758, A1759, A1760, A1761 G:A506, C:A507 A:A510
4tp6 A1618 fac-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1782, A1783, A1784
4tp6 A1640 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1884, A1885, A1886 C:A1501, G:A1504 U:A1506
4tp6 A1603 mer-3Oph A:A116(OP1), G:A117(OP2), G:A289(OP2) A1711, A1712, A1713 A:A288 G:A117, U:A118
4tp6 A1641 2Bout A1887, A1888, A1889, A1890, U101, U102 G:A1525, G:A1526
4tp6 A1627 Pout·2Rout A1827, A1828, A1829, A1830, A1831 U:A1345 C:A934, U:A1345
4tp6 A1637 Pout·2Bout A1870, A1871, A1872, A1873, A1874, A1875 G:A1385 G:A1386, G:A1385
4tp6 A1630 Pout·2Bout A1841, A1842, A1843, A1844, A1845, N201 A:A1360 A:A1360, C:A980
4tp6 A1623 Pout·3Bout A1807, A1808, A1809, A1810, A1811, A1812 A:A781 U:A798, G:A799, G:A800
4tp6 A1605 Pout·4Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259, C:A267
4tp6 A1612 Pout·4Bout A1752, A1753, A1754, A1755, A1756, A1757 A:A415 G:A417, U:A426, G:A425, G:A416
4tp6 A1620 2Pout·2Bout A1790, A1791, A1792, A1793, A1794, A1795 U:A644, G:A645 G:A645, G:A646
4tp6 A1606 2Pout·2Bout A1724, A1725, A1726, A1727, T101, T102 G:A258, G:A259 G:A259, G:A260
4tp6 A1622 2Pout·3Bout A1801, A1802, A1803, A1804, A1805, A1806 G:A803, U:A804 G:A771, U:A772, G:A773
4tp6 A1608 2Pout·3Bout A1732, A1733, A1734, A1735, A1736, A1737 A:A315, A:A329 G:A319, A:A320, G:A318
4tp6 A1631 3Pout A1846, A1847, A1848, A1849, A1850, N202 G:A1048, U:A1049, A:A1204
4tp6 A1615 4Pout·Rout A1766, A1767, A1768, A1769, A1770, A1771 C:A504, G:A537, C:A503, C:A536 C:A522

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
used for Mg2+
"Site type"		 Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen 		cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform 		Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

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