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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 4pe9




4PE9 (2.95Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to quinupristin. this file contains the 30s subunit of the first 70s ribosome.
List of all 38 Mg2+ binding sites in the PDB structure 4pe9 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
4pe9 A1621 Ob G:A1417(O6) A1797, A1798, A1799, A1800, A1801 G:A1416, G:A1415 G:A1416
4pe9 A1631 Nb G:A324(N7) A1842, A1843, A1844, A1845, T102 U:A323
4pe9 A1603 Nb G:A362(N7) A1712, A1713, A1714, A1715, L201 G:A361 G:A361
4pe9 A1626 2Nb G:A858(N7), G:A869(N7) A1822, A1823, A1824, A1825 G:A858, C:A857, C:A868, G:A869
4pe9 A1615 Oph A:A937(OP2) A1771, A1772, A1773, A1774, A1775 A:A938, G:A939
4pe9 A1625 Oph G:A21(OP1) A1817, A1818, A1819, A1820, A1821 G:A568, G:A567 G:A567, A:A573
4pe9 A1638 Oph G:A100(OP2) A1872, A1873, A1874, A1875, A1876 A:A101, G:A64, G:A100, G:A102
4pe9 A1606 Oph·Pout A:A547(OP1) A1726, A1727, A1728, A1729, A1730 G:A548 G:A402
4pe9 A1614 Oph·Pout C:A934(OP1) A1766, A1767, A1768, A1769, A1770 U:A1345 U:A1345
4pe9 A1633 Oph·Pout A:A608(OP2) A1850, A1851, A1852, A1853, A1854 A:A607 C:A631, A:A608, A:A609, A:A630, U:A610
4pe9 A1642 Oph·Pout C:A352(OP2) A1890, A1891, A1892, A1893, A1894 G:A354 C:A330, G:A331, C:A352 G:A354, A:A59
4pe9 A1612 Oph·2Pout A:A814(OP2) A1756, A1757, A1758, A1759, A1760 G:A577, A:A815 A:A816
4pe9 A1613 Oph·2Pout U:A891(OP2) A1761, A1762, A1763, A1764, A1765 A:A892, G:A903 A:A906, U:A904, U:A905
4pe9 A1634 Oph·2Pout A:A1110(OP2) A1855, A1856, A1857, A1858, A1859 C:A1109, A:A1111 U:A1189, A:A1110, A:A1111, C:A1112
4pe9 A1609 Oph·3Pout C:A578(OP1) A1739, A1740, A1741, A1742, A1743 C:A576, C:A817, U:A820 G:A575, G:A821
4pe9 A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
4pe9 A1630 Oph·Ob G:A558(OP1) G:A299(O6) A1838, A1839, A1840, A1841 A:A560 G:A297 A:A298, A:A300, G:A566
4pe9 A1632 Oph·Ob A:A533(OP1) U:A516(O4) A1846, A1847, A1848, A1849 A:A532 G:A515
4pe9 A1635 Oph·Ob U:A1095(OP2) G:A1108(O6) A1860, A1861, A1862, A1863 C:A1096 G:A1094 C:A1109
4pe9 A1639 Oph·Ob A:A195(OP2) U:A180(O4) A1877, A1878, A1879, A1880 C:A194, A:A179 A:A181

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>