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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 2i2u



2I2U (3.22Å) -- RIBOSOME : Crystal structure of ribosome with messenger rna and the anticodon stem-loop of p-site trna. 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 55 Mg2+ binding sites in the PDB structure 2i2u 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
2i2u A1594 Ob G:A1108(O6) A1847, A1848, A1849, A1850 U:A1095, C:A1096 G:A1094
2i2u A1576 Ob G:A1417(O6) A1755, A1756, A1757, A1758, A1759 G:A1416, G:A1415 G:A1482, G:A1415, G:A1416
2i2u A1549 Nb G:A362(N7) A1628, A1629, A1630, A1631, L124 G:A362 G:A361 G:A361
2i2u A1584 Nb G:A1050(N7) A1800, A1801, A1802, A1803, A1804 U:A1049 G:A1048, C:A1051
2i2u A1563 Nb G:A324(N7) A1695, A1696, A1697, A1698, A1699 G:A324, U:A323
2i2u A1560 2Nb G:A858(N7), G:A869(N7) A1682, A1683, A1684, A1685 G:A869, G:A858, C:A868, C:A857
2i2u A1557 Oph A:A572(OP1) A1668, A1669, A1670, A1671, A1672 A:A819
2i2u A1592 Oph·Pout A:A1110(OP2) A1838, A1839, A1840, A1841, A1842 C:A1109 A:A1111
2i2u A1578 Oph·Pout C:A934(OP1) A1766, A1767, A1768, A1769, A1770 U:A1345 U:A1345
2i2u A1573 Oph·Pout C:A352(OP2) A1740, A1741, A1742, A1743, A1744 G:A354 C:A330, C:A352, G:A331 C:A330, G:A354, A:A59
2i2u A1568 Oph·Pout G:A100(OP2) A1717, A1718, A1719, A1720, A1721 A:A101 G:A64, A:A101, G:A102
2i2u A1565 Oph·Pout A:A608(OP2) A1704, A1705, A1706, A1707, A1708 A:A609 A:A630, A:A609, C:A631, U:A610
2i2u A1558 Oph·Pout G:A21(OP1) A1673, A1674, A1675, A1676, A1677 U:A561 G:A568, G:A567 A:A573, G:A567
2i2u A1595 Oph·Pout U:A1224(OP1) A1851, A1852, A1853, A1854, A1855 G:A951 C:A1223 C:A1223, A:A977, A:A974
2i2u A1561 Oph·Pout A:A1433(OP2) A1686, A1687, A1688, A1689, A1690 A:A1434 A:A1434, G:A1435
2i2u A1543 Oph·2Pout U:A891(OP2) A1599, A1600, A1601, A1602, A1603 A:A892, G:A903 U:A905, A:A906, U:A904
2i2u X358 Oph·2Pout U:X6(OP1) A1868, A1869, X281, X282, X284 C:A1496, U:X5 U:X6 G:A1497
2i2u A1571 Oph·2Pout C:A536(OP1) A1732, A1733, A1734, A1735, A1736 C:A504, G:A537 C:A522
2i2u A1551 Oph·3Pout C:A578(OP1) A1635, A1636, A1637, A1638, A1639 C:A817, C:A576, U:A820 G:A575
2i2u A1547 Oph·3Pout A:A560(OP2) A1617, A1618, A1619, A1620, A1621 U:A562, A:A563, G:A557 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>