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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 4tp4




4TP4 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to virginiamycin m1. this file contains the 30s subunit of the first 70s ribosome.
List of all 40 Mg2+ binding sites in the PDB structure 4tp4 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
4tp4 A1631 Ob U:A516(O4) A1845, A1846, A1847, A1848 A:A533 C:A514, G:A515, G:A517
4tp4 A1620 Ob G:A1417(O6) A1796, A1797, A1798, A1799, A1800 G:A1416, G:A1415 G:A1416, U:A1481, G:A1482
4tp4 A1603 Nb G:A362(N7) A1712, A1713, A1714, A1715, L201 G:A361, G:A362 G:A361
4tp4 A1630 Nb G:A324(N7) A1841, A1842, A1843, A1844, T102 G:A324
4tp4 A1625 2Nb G:A858(N7), G:A869(N7) A1821, A1822, A1823, A1824 G:A858, G:A869, C:A857, C:A868
4tp4 A1615 Oph A:A937(OP2) A1771, A1772, A1773, A1774, A1775 A:A938, G:A939
4tp4 A1624 Oph G:A21(OP1) A1816, A1817, A1818, A1819, A1820 G:A568, G:A567 A:A563, A:A573, G:A567
4tp4 A1606 Oph·Pout A:A547(OP1) A1726, A1727, A1728, A1729, A1730 G:A548 G:A402
4tp4 A1614 Oph·Pout C:A934(OP1) A1766, A1767, A1768, A1769, A1770 U:A1345
4tp4 A1637 Oph·Pout G:A100(OP2) A1871, A1872, A1873, A1874, A1875 A:A101 A:A101, G:A64, G:A100, G:A102
4tp4 A1612 Oph·2Pout A:A814(OP2) A1756, A1757, A1758, A1759, A1760 A:A815, G:A577 A:A816
4tp4 A1613 Oph·2Pout U:A891(OP2) A1761, A1762, A1763, A1764, A1765 A:A892, G:A903 A:A906, U:A905, U:A904
4tp4 A1632 Oph·2Pout A:A608(OP2) A1849, A1850, A1851, A1852, A1853 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
4tp4 A1633 Oph·2Pout A:A1110(OP2) A1854, A1855, A1856, A1857, A1858 C:A1109, A:A1111 U:A1189, A:A1110, A:A1111
4tp4 A1609 Oph·3Pout C:A578(OP1) A1739, A1740, A1741, A1742, A1743 C:A576, C:A817, U:A820 G:A575
4tp4 A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 G:A566
4tp4 A1629 Oph·Ob G:A558(OP1) G:A299(O6) A1837, A1838, A1839, A1840 A:A560 G:A297 A:A300, G:A566
4tp4 A1634 Oph·Ob U:A1095(OP2) G:A1108(O6) A1859, A1860, A1861, A1862 C:A1096 G:A1094
4tp4 A1638 Oph·Ob A:A195(OP2) U:A180(O4) A1876, A1877, A1878, A1879 C:A194 A:A181
4tp4 A1608 cis-2Oph A:A573(OP2), A:A574(OP2) A1736, A1737, A1738 U:A571, A:A572 A:A574

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>