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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 4tol



4TOL (3Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to linopristin. this file contains the 30s subunit of the first 70s ribosome.
List of all 37 Mg2+ binding sites in the PDB structure 4tol 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
4tol A1621 Ob G:A1417(O6) A1797, A1798, A1799, A1800, A1801 G:A1416, G:A1415 G:A1416
4tol A1632 Ob U:A516(O4) A1846, A1847, A1848, A1849 A:A533 G:A515
4tol A1603 Nb G:A362(N7) A1712, A1713, A1714, A1715, L201 G:A361, G:A362 G:A361
4tol A1631 Nb G:A324(N7) A1842, A1843, A1844, A1845, T102 U:A323, G:A326, G:A324
4tol A1626 2Nb G:A858(N7), G:A869(N7) A1822, A1823, A1824, A1825 G:A858, C:A868, C:A857
4tol A1615 Oph A:A937(OP2) A1771, A1772, A1773, A1774, A1775 A:A938, G:A939
4tol A1635 Oph U:A1095(OP2) A1860, A1861, A1862, A1863 G:A1094 G:A1094, G:A1108
4tol A1638 Oph G:A100(OP2) A1872, A1873, A1874, A1875, A1876 G:A100, G:A64
4tol A1606 Oph·Pout A:A547(OP1) A1726, A1727, A1728, A1729, A1730 G:A548
4tol A1614 Oph·Pout C:A934(OP1) A1766, A1767, A1768, A1769, A1770 U:A1345 U:A1345
4tol A1620 Oph·Pout G:A1304(OP2) A1793, A1794, A1795, A1796 C:A1303 G:A1305
4tol A1625 Oph·Pout G:A21(OP1) A1817, A1818, A1819, A1820, A1821 U:A561 G:A568, G:A567 A:A573, G:A567, A:A563
4tol A1633 Oph·Pout A:A608(OP2) A1850, A1851, A1852, A1853, A1854 A:A607 C:A631, A:A609, U:A610
4tol A1642 Oph·Pout C:A352(OP2) A1890, A1891, A1892, A1893, A1894 G:A354 C:A352, G:A331 G:A354, A:A59
4tol A1613 Oph·2Pout U:A891(OP2) A1761, A1762, A1763, A1764, A1765 G:A903, A:A892 U:A905, A:A906, U:A904
4tol A1634 Oph·2Pout A:A1110(OP2) A1855, A1856, A1857, A1858, A1859 C:A1109, A:A1111 A:A1110, A:A1111, U:A1065, U:A1189, C:A1112
4tol A1609 Oph·3Pout C:A578(OP1) A1739, A1740, A1741, A1742, A1743 C:A817, C:A576, U:A820 G:A575
4tol A1628 Oph·3Pout A:A964(OP1) A1832, A1833, A1834, A1835 U:A965, U:A1199, G:A1198
4tol A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A558, G:A557
4tol A1630 Oph·Ob G:A558(OP1) G:A299(O6) A1838, A1839, A1840, A1841 A:A560 G:A297 A:A300, G:A566

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/)
For any help please contact <dust@iwonka.med.virginia.edu>