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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 2avy



2AVY (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli at 3.5 a resolution. this file contains the 30s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes and is described in remark 400.
List of all 59 Mg2+ binding sites in the PDB structure 2avy 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
2avy A1601 Ob G:A1417(O6) A1885, A1886, A1887, A1888, A1889 G:A1416, G:A1415 G:A1416, G:A1482
2avy A1574 Ob G:A1370(O6) A1756, A1757, A1758, A1759, A1760 G:A1371, U:A1351, C:A1352
2avy A1561 Ob G:A1050(O6) A1688, A1689, A1690, A1691, A1692 G:A1207, C:A1051, G:A1048
2avy A1600 Ob U:A1358(O4) A1880, A1881, A1882, A1883, A1884 A:A1357 A:A1357, G:A976, C:A1359
2avy A1560 Nb G:A362(N7) A1683, A1684, A1685, A1686, A1687 G:A361, G:A362 G:A361
2avy A1580 Nb G:A324(N7) A1782, A1783, A1784, A1785, A1786 U:A323, G:A324
2avy A1572 2Nb G:A858(N7), G:A869(N7) A1746, A1747, A1748, A1749 G:A858, G:A869, C:A868
2avy A1570 Oph G:A21(OP1) A1737, A1738, A1739, A1740, A1741 G:A567 A:A573, G:A567
2avy A1595 Oph C:A352(OP2) A1852, A1853, A1854, A1855, A1856 G:A331, C:A330 C:A330, G:A354, A:A59
2avy A1590 Oph G:A100(OP2) A1829, A1830, A1831, A1832, A1833 G:A64, C:A99, G:A100, A:A101
2avy A1554 Oph A:A937(OP2) A1654, A1655, A1656, A1657, A1658 G:A939
2avy A1547 Oph·Pout C:A934(OP1) A1622, A1623, A1624, A1625, A1626 U:A1345
2avy A1577 Oph·Pout A:A1433(OP2) A1767, A1768, A1769, A1770, A1771 A:A1434 A:A1434, G:A1435
2avy A1568 Oph·2Pout A:A768(OP2) A1727, A1728, A1729, A1730, A1731 A:A767, U:A804 G:A769
2avy A1593 Oph·2Pout C:A536(OP1) A1844, A1845, A1846, A1847, A1848 C:A504, G:A537 C:A522
2avy A1586 Oph·2Pout U:A1224(OP1) A1809, A1810, A1811, A1812, A1813 G:A951, U:A952 A:A977
2avy A1583 Oph·2Pout A:A1110(OP2) A1796, A1797, A1798, A1799, A1800 C:A1109, A:A1111 U:A1189, C:A1112
2avy A1582 Oph·2Pout A:A608(OP2) A1791, A1792, A1793, A1794, A1795 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
2avy A1569 Oph·2Pout A:A572(OP1) A1732, A1733, A1734, A1735, A1736 A:A573, G:A917 A:A819
2avy A1543 Oph·2Pout C:A578(OP1) A1602, A1603, A1604, A1605, A1606 C:A817, C:A576 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/)
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