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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 2qbh



2QBH (4Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with gentamicin and ribosome recycling factor (rrf). this file contains the 30s subunit of the first 70s ribosome, with gentamicin bound. the entire crystal structure contains
List of all 56 Mg2+ binding sites in the PDB structure 2qbh 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
2qbh A1602 Ob G:A1417(O6) A1888, A1889, A1890, A1891, A1892 G:A1416, G:A1415 G:A1416, U:A1481, G:A1482
2qbh A1601 Ob U:A1358(O4) A1883, A1884, A1885, A1886, A1887 C:A1359, A:A1357
2qbh A1586 Ob G:A1108(O6) A1808, A1809, A1810, A1811 U:A1095 G:A1106, C:A1107
2qbh A1575 Ob G:A1370(O6) A1760, A1761, A1762, A1763, A1764 G:A1371, U:A1351
2qbh A1581 Nb G:A324(N7) A1786, A1787, A1788, A1789, T236 U:A323, G:A324
2qbh A1560 Nb G:A362(N7) A1685, A1686, A1687, L124, L125 G:A362, A:A364
2qbh A1573 2Nb G:A858(N7), G:A869(N7) A1750, A1751, A1752, A1753 G:A858, G:A869, C:A868
2qbh A1571 Oph G:A21(OP1) A1741, A1742, A1743, A1744, A1745 A:A573, A:A563, G:A567
2qbh A1554 Oph A:A937(OP2) A1656, A1657, A1658, A1659, A1660
2qbh A1578 Oph A:A1433(OP2) A1771, A1772, A1773, A1774, A1775 G:A1432 A:A1434, G:A1435
2qbh A1570 Oph·Pout A:A572(OP1) A1736, A1737, A1738, A1739, A1740 A:A573 A:A819
2qbh A1583 Oph·Pout A:A608(OP2) A1794, A1795, A1796, A1797, A1798 A:A609 A:A630, C:A631, A:A609, U:A610
2qbh A1547 Oph·Pout C:A934(OP1) A1624, A1625, A1626, A1627, A1628 U:A1345
2qbh A1596 Oph·Pout C:A352(OP2) A1855, A1856, A1857, A1858, A1859 G:A354 G:A331, C:A352, C:A330 C:A330, A:A59
2qbh A1591 Oph·Pout G:A100(OP2) A1832, A1833, A1834, A1835, A1836 A:A101 G:A64, G:A100, A:A101
2qbh A1584 Oph·2Pout A:A1110(OP2) A1799, A1800, A1801, A1802, A1803 C:A1109, A:A1111 A:A1110, A:A1111, U:A1189
2qbh A1597 Oph·2Pout G:A111(OP2) A1860, A1861, A1862, A1863, A1864 C:A110, G:A112 G:A112, G:A111
2qbh A1594 Oph·2Pout C:A536(OP1) A1847, A1848, A1849, A1850, A1851 C:A504, G:A537 C:A522
2qbh A1587 Oph·2Pout U:A1224(OP1) A1812, A1813, A1814, A1815, A1816 G:A951, U:A952 A:A977
2qbh A1543 Oph·3Pout C:A578(OP1) A1604, A1605, A1606, A1607, A1608 C:A576, C:A817, U:A820 G:A575

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>