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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 4gd1



4GD1 (3Å) -- RIBOSOME : Structures of the bacterial ribosome in classical and hybrid states of trna binding
List of all 30 Mg2+ binding sites in the PDB structure 4gd1 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
4gd1 A1621 Ob G:A1417(O6) A1799, A1800, A1801, A1802, A1803 G:A1416, G:A1415 G:A1416
4gd1 A1631 Nb G:A324(N7) A1844, A1845, A1846, A1847, A1848 G:A326
4gd1 A1603 Nb G:A362(N7) A1712, A1713, A1714, A1715, A1716 G:A362 G:A361
4gd1 A1625 Oph G:A21(OP1) A1819, A1820, A1821, A1822, A1823 G:A568, G:A567 G:A567, A:A573
4gd1 A1638 Oph G:A100(OP2) A1875, A1876, A1877, A1878, A1879 A:A101, G:A64, C:A99, G:A100
4gd1 A1614 Oph·Pout C:A934(OP1) A1767, A1768, A1769, A1770, A1771 U:A1345 U:A1345
4gd1 A1606 Oph·Pout A:A547(OP1) A1727, A1728, A1729, A1730, A1731 G:A548 G:A402
4gd1 A1615 Oph·Pout A:A937(OP2) A1772, A1773, A1774, A1775, A1776 A:A938 A:A937, A:A938, G:A939
4gd1 A1642 Oph·Pout C:A352(OP2) A1893, A1894, A1895, A1896, A1897 G:A354 G:A331, C:A352 A:A59, G:A354
4gd1 A1613 Oph·2Pout U:A891(OP2) A1762, A1763, A1764, A1765, A1766 G:A903, A:A892 U:A905, A:A906, U:A904
4gd1 A1633 Oph·2Pout A:A608(OP2) A1853, A1854, A1855, A1856, A1857 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
4gd1 A1607 Oph·3Pout A:A560(OP2) A1732, A1733, A1734, A1735, A1736 U:A562, G:A557, G:A558 A:A559 G:A566
4gd1 A1639 Oph·Ob A:A195(OP2) U:A180(O4) A1880, A1881, A1882, A1883 C:A194, A:A179 A:A181, A:A179
4gd1 A1630 Oph·Ob G:A558(OP1) G:A299(O6) A1840, A1841, A1842, A1843 A:A560 G:A297 G:A566
4gd1 A1632 Oph·Ob A:A533(OP1) U:A516(O4) A1849, A1850, A1851, A1852 C:A514 G:A515
4gd1 A1635 Oph·Ob U:A1095(OP2) G:A1108(O6) A1863, A1864, A1865, A1866 C:A1096 G:A1094 G:A1068
4gd1 A1620 cis-2Oph C:A1303(OP1), G:A1304(OP2) A1795, A1796, A1797, A1798 G:A1242 G:A1305
4gd1 A1618 cis-2Oph C:A1054(OP2), A:A1197(OP2) A1785, A1786, A1787, A1788 G:A1053 G:A1198, A:A1197
4gd1 A1627 2Bout A1828, A1829, A1830, A1831, A1832, A1833 G:A1386, G:A1385
4gd1 A1636 4Bout A1867, A1868, A1869, A1870, A1871, U101 G:A1525, C:A1524, G:A1526, C:A1509

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].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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