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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 1vs7



1VS7 (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with the antibiotic kasugamyin at 3.5a resolution. this file contains the 30s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes and is
List of all 60 Mg2+ binding sites in the PDB structure 1vs7 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
1vs7 A1605 Ob G:A1417(O6) A1901, A1902, A1903, A1904, A1905 G:A1416, G:A1415 G:A1482, G:A1416
1vs7 A1580 Ob G:A1370(O6) A1787, A1788, A1789, A1790, A1791 U:A1351, G:A1371
1vs7 A1585 Nb G:A324(N7) A1807, A1808, A1809, A1810, A1811 G:A324, G:A326, U:A323
1vs7 A1550 Nb G:A362(N7) A1635, A1636, A1637, L124, L125 G:A361, G:A362 G:A361
1vs7 A1578 2Nb G:A858(N7), G:A869(N7) A1777, A1778, A1779, A1780 G:A869, G:A858, C:A868
1vs7 A1576 Oph G:A21(OP1) A1768, A1769, A1770, A1771, A1772 G:A568, G:A567 A:A573, G:A567
1vs7 A1565 Oph A:A937(OP2) A1707, A1708, A1709, A1710, A1711 G:A939
1vs7 A1604 Oph C:A980(OP1) A1896, A1897, A1898, A1899, A1900 G:A1221, G:A1220, A:A1219
1vs7 A1575 Oph A:A572(OP1) A1763, A1764, A1765, A1766, A1767 A:A819
1vs7 A1587 Oph A:A608(OP2) A1816, A1817, A1818, A1819, A1820 A:A630, A:A609, C:A631, U:A610
1vs7 A1600 Oph·Pout C:A352(OP2) A1876, A1877, A1878, A1879, A1880 G:A354 C:A330, C:A352, G:A331 C:A330, G:A354, A:A59
1vs7 A1595 Oph·Pout G:A100(OP2) A1853, A1854, A1855, A1856, A1857 A:A101 C:A99, G:A100, A:A101, G:A64
1vs7 A1583 Oph·Pout A:A1433(OP2) A1798, A1799, A1800, A1801, A1802 A:A1434 A:A1434, G:A1435
1vs7 A1601 Oph·Pout G:A111(OP2) A1881, A1882, A1883, A1884, A1885 C:A110 G:A112
1vs7 A1553 Oph·Pout C:A934(OP1) A1650, A1651, A1652, A1653, A1654 U:A1345
1vs7 A1561 Oph·Pout C:A578(OP1) A1684, A1685, A1686, A1687, A1688 C:A817 G:A575
1vs7 A1598 Oph·2Pout C:A536(OP1) A1868, A1869, A1870, A1871, A1872 C:A504, G:A537 C:A522
1vs7 A1591 Oph·2Pout U:A1224(OP1) A1834, A1835, A1836, A1837 G:A951, U:A952 C:A1223
1vs7 A1588 Oph·2Pout A:A1110(OP2) A1821, A1822, A1823, A1824, A1825 C:A1109, A:A1111 A:A1110, A:A1111, U:A1189
1vs7 A1554 Oph·2Pout C:A1195(OP1) A1655, A1656, A1657, A1658, A1659 A:A1196, A:A1398 A:A1398

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>