MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON 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 3 of 3 | « Previous | Next » | 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 A1561 2Bout E168, A1688, A1689, A1690, A1691, A1692 U:A1076, G:A1077 2qbf A1590 3Bout A1838, A1839, A1840, A1841, A1842, A1843 C:A1509, G:A1525, G:A1526 2qbf A1566 3Bout A1716, A1717, A1718, A1719, A1720, A1721 G:A257, G:A258, G:A259 2qbf A1557 3Bout A1671, A1672, A1673, A1674, A1675, A1676 G:A1048, G:A1050, C:A1051 2qbf A1551 Pout·Bout A1644, A1645, A1646, A1647, A1648, A1649 A:A172 G:A148 2qbf A1568 Pout·Bout A1733, A1734, A1735, A1736, A1737, A1738 G:A727 G:A727 2qbf A1558 Pout·2Bout N103, N104, A1677, A1678, A1679 A:A1360 C:A980, G:A1361 2qbf A1546 Pout·2Bout A1616, A1617, A1618, A1619, A1620, A1621 G:A803 G:A771, U:A772 2qbf A1567 Pout·3Bout A1722, A1723, A1724, A1725, A1726, A1727 A:A781 G:A800, U:A798, G:A799 2qbf A1562 Pout·3Bout A1693, A1694, A1695, A1696, A1697, A1698 U:A644 G:A645, G:A592, G:A646 2qbf A1591 2Pout A1844, A1845, A1846, A1847, A1848, A1849 A:A553, U:A552 2qbf E167 2Pout·Bout A1728, A1729, A1730, A1731, A1732 U:A20, G:A21 G:A21 2qbf A1601 2Pout·Bout T358, A1892, A1893, A1894, A1895, A1896 G:A259, G:A258 G:A259 2qbf A1563 2Pout·2Bout A1699, A1700, A1701, A1702, A1703, A1704 A:A329, A:A315 G:A319, A:A320 2qbf A1548 3Pout A1627, A1628, A1629, A1630, A1631, A1632 G:A15, U:A13, U:A14 2qbf A1550 3Pout A1638, A1639, A1640, A1641, A1642, A1643 U:A333, G:A350, C:A334 2qbf A1600 3Pout·2Bout A1886, A1887, A1888, A1889, A1890, A1891 A:A1394, G:A917, A:A918 A:A918, A:A919 2qbf A1556 4Pout N101, N102, A1667, A1668, A1669, A1670 G:A1048, U:A1049, C:A1203, A:A1204 2qbf A1596 4Pout·Rout A1868, A1869, A1870, A1871, A1872 C:A536, G:A537, A:A523, C:A503 C:A522 2qbf A1572 4Pout·2Bout A1757, A1758, A1759, A1760, A1761, A1762 A:A768, U:A804, C:A805, A:A767 G:A769, A:A768

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].

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