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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 4tpc



4TPC (2.8Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to flopristin and linopristin. this file contains the 30s subunit of the first 70s ribosome.
List of all 40 Mg2+ binding sites in the PDB structure 4tpc 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
4tpc A1632 Ob U:A516(O4) A1846, A1847, A1848, A1849 A:A533 C:A514, G:A515
4tpc A1621 Ob G:A1417(O6) A1797, A1798, A1799, A1800, A1801 G:A1416, G:A1415 G:A1416, G:A1482
4tpc A1603 Nb G:A362(N7) A1712, A1713, A1714, A1715, L201 G:A361, G:A362 G:A361
4tpc A1631 Nb G:A324(N7) A1842, A1843, A1844, A1845, T102
4tpc A1626 2Nb G:A858(N7), G:A869(N7) A1822, A1823, A1824, A1825 G:A858, G:A869, C:A857, C:A868
4tpc A1615 Oph A:A937(OP2) A1771, A1772, A1773, A1774, A1775 A:A938, G:A939
4tpc A1614 Oph·Pout C:A934(OP1) A1766, A1767, A1768, A1769, A1770 U:A1345
4tpc A1625 Oph·Pout G:A21(OP1) A1817, A1818, A1819, A1820, A1821 U:A561 G:A567 A:A563, A:A573, G:A567
4tpc A1638 Oph·Pout G:A100(OP2) A1872, A1873, A1874, A1875, A1876 A:A101 G:A64, G:A100, G:A102
4tpc A1606 Oph·Pout A:A547(OP1) A1726, A1727, A1728, A1729, A1730 G:A548 C:A403, G:A402
4tpc A1613 Oph·2Pout U:A891(OP2) A1761, A1762, A1763, A1764, A1765 A:A892, G:A903 A:A906, U:A904, U:A905
4tpc A1633 Oph·2Pout A:A608(OP2) A1850, A1851, A1852, A1853, A1854 A:A607, A:A609 C:A631, A:A609, A:A608, U:A610
4tpc A1634 Oph·2Pout A:A1110(OP2) A1855, A1856, A1857, A1858, A1859 C:A1109, A:A1111 U:A1189, A:A1110, A:A1111
4tpc A1612 Oph·2Pout A:A814(OP2) A1756, A1757, A1758, A1759, A1760 G:A577, A:A815
4tpc A1609 Oph·3Pout C:A578(OP1) A1739, A1740, A1741, A1742, A1743 C:A576, C:A817, U:A820 G:A575
4tpc A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 G:A566
4tpc A1630 Oph·Ob G:A558(OP1) G:A299(O6) A1838, A1839, A1840, A1841 G:A297 A:A300, G:A566
4tpc A1635 Oph·Ob U:A1095(OP2) G:A1108(O6) A1860, A1861, A1862, A1863 C:A1096 G:A1094 G:A1094, C:A1109
4tpc A1639 Oph·Ob A:A195(OP2) U:A180(O4) A1877, A1878, A1879, A1880 C:A194, A:A179 A:A181
4tpc A1620 cis-2Oph C:A1303(OP1), G:A1304(OP2) A1793, A1794, A1795, A1796 G:A1242 G:A1304, G:A1305

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>