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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 4gaq



4GAQ (3.3Å) -- RIBOSOME/ANTIBIOTIC : Allosteric control of the ribosome by small-molecule antibiotics
List of all 36 Mg2+ binding sites in the PDB structure 4gaq 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"
Page 1 of 2 | « Previous | | 1 | 2
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4gaq A1630 Or G:A1053(O2') A1847, A1848, A1849, A1850 C:A1054, A:A1197, G:A1198
4gaq A1636 Ob G:A1417(O6) A1872, A1873, A1874, A1875, A1876 G:A1416, G:A1415 G:A1482
4gaq A1610 Nb G:A324(N7) A1739, A1740, A1741, A1742, A1743 G:A326
4gaq A1612 Nb G:A362(N7) A1749, A1750, A1751, A1752, A1753 G:A361, G:A362 G:A361
4gaq A1625 2Nb G:A858(N7), G:A869(N7) A1817, A1818, A1819, A1820 G:A858, G:A869, C:A857
4gaq A1602 Oph G:A21(OP1) A1701, A1702, A1703, A1704, A1705 G:A567, G:A568 A:A563, A:A573, G:A567
4gaq A1603 Oph G:A100(OP2) A1706, A1707, A1708, A1709, A1710 A:A101, G:A64, G:A100, G:A102
4gaq A1621 Oph·Pout A:A608(OP2) A1796, A1797, A1798, A1799, A1800 A:A607 G:A292 C:A631, A:A609, U:A610, A:A630
4gaq A1628 Oph·Pout A:A937(OP2) A1831, A1832, A1833, A1834, A1835 A:A938 A:A938, G:A939
4gaq A1631 Oph·Pout C:A1096(OP2) A1851, A1852, A1853, A1854 U:A1095 G:A1108, C:A1109
4gaq A1634 Oph·Pout C:A1303(OP1) A1862, A1863, A1864, A1865 G:A1304 G:A1305, G:A1304
4gaq A1611 Oph·Pout C:A352(OP2) A1744, A1745, A1746, A1747, A1748 G:A354 C:A352, C:A330, G:A331 G:A354, C:A330, A:A59
4gaq A1627 Oph·2Pout U:A1345(OP1) A1826, A1827, A1828, A1829, A1830 C:A934, A:A1346
4gaq A1605 Oph·2Pout A:A179(OP2) A1714, A1715, A1716, A1717 C:A178, C:A194 C:A193
4gaq A1632 Oph·2Pout A:A1110(OP2) A1855, A1856, A1857, A1858, A1859 C:A1109, A:A1111 A:A1188, U:A1189, A:A1110, A:A1111, C:A1112
4gaq A1624 Oph·2Pout A:A814(OP2) A1812, A1813, A1814, A1815, A1816 G:A577, A:A815 A:A816
4gaq A1614 Oph·3Pout G:A506(OP2) A1760, A1761, A1762, A1763 A:A509, C:A507, A:A510 U:A508 A:A510
4gaq A1617 Oph·3Pout A:A560(OP2) A1777, A1778, A1779, A1780, A1781 G:A557, G:A558, A:A563 A:A300, G:A566
4gaq A1619 Oph·4Pout C:A578(OP1) A1785, A1786, A1787, A1788, A1789 U:A820, G:A821, C:A817, C:A576 G:A575
4gaq A1608 Oph·Ob G:A558(OP1) G:A299(O6) A1729, A1730, A1731, A1732 G:A297 A:A300

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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