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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 2qbf



2QBF (3.3Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with ribosome recycling factor (rrf). this file contains the 30s subunit of the second 70s ribosome. the entire crystal structure contains two 70s ribosomes and is described in
List of all 60 Mg2+ binding sites in the PDB structure 2qbf 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 3 | « Previous | | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qbf A1603 Ob G:A1417(O6) A1902, A1903, A1904, A1905, A1906 G:A1415 G:A1482, G:A1415, G:A1416
2qbf A1578 Ob G:A1370(O6) A1787, A1788, A1789, A1790, A1791 G:A1371, U:A1372, U:A1351
2qbf A1583 Nb G:A324(N7) A1807, A1808, A1809, A1810, A1811 U:A323, G:A324
2qbf A1549 Nb G:A362(N7) A1633, A1634, A1635, A1636, A1637 G:A361, G:A362 G:A361
2qbf A1576 2Nb G:A858(N7), G:A869(N7) A1777, A1778, A1779, A1780 G:A869, G:A858, C:A868, C:A857
2qbf A1564 Oph A:A937(OP2) A1705, A1706, A1707, A1708, A1709 A:A937, A:A938, G:A939
2qbf A1574 Oph G:A21(OP1) A1768, A1769, A1770, A1771, A1772 G:A568, G:A567 A:A573, G:A567
2qbf A1553 Oph C:A1195(OP1) A1655, A1656, A1657, A1658, A1659 A:A1398
2qbf A1593 Oph G:A100(OP2) A1853, A1854, A1855, A1856, A1857 G:A64, A:A101
2qbf A1598 Oph·Pout C:A352(OP2) A1876, A1877, A1878, A1879, A1880 G:A354 C:A330, C:A352, G:A331 C:A330, G:A354, A:A59
2qbf A1585 Oph·Pout A:A608(OP2) A1816, A1817, A1818, A1819, A1820 A:A609 A:A630, A:A608, A:A609, C:A631, U:A610
2qbf A1581 Oph·Pout A:A1433(OP2) A1798, A1799, A1800, A1801, A1802 A:A1434 A:A1434, G:A1435
2qbf A1573 Oph·Pout A:A572(OP1) A1763, A1764, A1765, A1766, A1767 A:A573 A:A819
2qbf A1599 Oph·Pout G:A111(OP2) A1881, A1882, A1883, A1884, A1885 C:A110 G:A111, G:A112
2qbf A1552 Oph·Pout C:A934(OP1) A1650, A1651, A1652, A1653, A1654 U:A1345 U:A1345
2qbf A1602 Oph·Pout C:A980(OP1) A1897, A1898, A1899, A1900, A1901 A:A1219 G:A1220, G:A1221, A:A1219
2qbf A1543 Oph·2Pout U:A891(OP2) A1604, A1605, A1606, A1607, A1608 A:A892, G:A903 U:A905, A:A906, U:A904
2qbf A1586 Oph·2Pout A:A1110(OP2) A1821, A1822, A1823, A1824, A1825 C:A1109, A:A1111 A:A1110, A:A1111, U:A1189
2qbf A1560 Oph·3Pout C:A578(OP1) A1683, A1684, A1685, A1686, A1687 C:A817, C:A576, U:A820 G:A575
2qbf A1547 Oph·3Pout A:A560(OP2) A1622, A1623, A1624, A1625, A1626 U:A562, A:A563, G:A557 A:A559 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>