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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 4tp6



4TP6 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to virginiamycin m1. this file contains the 30s subunit of the second 70s ribosome.
List of all 39 Mg2+ binding sites in the PDB structure 4tp6 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4tp6 A1638 Ob G:A1417(O6) A1876, A1877, A1878, A1879, A1880 G:A1416, G:A1415 G:A1416, U:A1481
4tp6 A1611 Nb G:A362(N7) A1748, A1749, A1750, A1751, L201 G:A361, G:A362 G:A361
4tp6 A1609 Nb G:A324(N7) A1738, A1739, A1740, A1741, A1742 U:A323, G:A324
4tp6 A1625 2Nb G:A858(N7), G:A869(N7) A1818, A1819, A1820, A1821 G:A858, G:A869, C:A868
4tp6 A1602 Oph G:A100(OP2) A1706, A1707, A1708, A1709, A1710 G:A100, A:A101, G:A64
4tp6 A1628 Oph A:A937(OP2) A1832, A1833, A1834, A1835, A1836 A:A937, A:A938, G:A939
4tp6 A1632 Oph C:A1054(OP2) A1851, A1852, A1853, A1854 G:A1053 G:A1198
4tp6 A1633 Oph U:A1095(OP2) A1855, A1856, A1857, A1858 G:A1108
4tp6 A1601 Oph G:A21(OP1) A1701, A1702, A1703, A1704, A1705 G:A567, G:A568 A:A573, G:A567
4tp6 A1616 Oph·Pout A:A547(OP1) A1772, A1773, A1774, A1775, A1776 G:A548 G:A402
4tp6 A1610 Oph·Pout C:A352(OP2) A1743, A1744, A1745, A1746, A1747 G:A354 C:A330, G:A331 G:A354, C:A330, A:A59
4tp6 A1624 Oph·2Pout A:A814(OP2) A1813, A1814, A1815, A1816, A1817 A:A815, G:A577 A:A816
4tp6 A1634 Oph·2Pout A:A1110(OP2) A1859, A1860, A1861, A1862, A1863 C:A1109, A:A1111 U:A1189, A:A1110, A:A1111, C:A1112
4tp6 A1636 Oph·2Pout C:A1303(OP2) A1866, A1867, A1868, A1869 G:A1304, G:A1305 G:A1305
4tp6 A1626 Oph·2Pout U:A891(OP2) A1822, A1823, A1824, A1825, A1826 A:A892, G:A903 A:A906, U:A904, U:A905
4tp6 A1621 Oph·2Pout A:A608(OP2) A1796, A1797, A1798, A1799, A1800 A:A607, A:A609 A:A609, U:A610, A:A630, A:A608
4tp6 A1629 Oph·3Pout A:A964(OP1) A1837, A1838, A1839, A1840 U:A965, G:A1198, U:A1199
4tp6 A1617 Oph·3Pout A:A560(OP2) A1777, A1778, A1779, A1780, A1781 U:A562, G:A557, G:A558 A:A559 G:A566
4tp6 A1619 Oph·3Pout C:A578(OP1) A1785, A1786, A1787, A1788, A1789 C:A817, C:A576, U:A820 G:A575
4tp6 A1614 Oph·Ob A:A533(OP1) U:A516(O4) A1762, A1763, A1764, A1765 G:A517, G:A515

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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