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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 4tp8



4TP8 (2.8Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to dalfopristin and quinupristin. this file contains the 30s subunit of the first 70s ribosome.
List of all 41 Mg2+ binding sites in the PDB structure 4tp8 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
4tp8 A1628 cis-2Oph A:A964(OP1), U:A1199(OP1) A1831, A1832, A1833, A1834 U:A965, G:A1198
4tp8 A1605 cis-2Oph A:A509(OP2), A:A510(OP2) A1721, A1722, A1723, A1724 G:A506, C:A507 A:A510
4tp8 A1637 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP1) A1869, A1870, A1871 G:A1504, U:A1498 A:A1500
4tp8 A1641 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1887, A1888, A1889 A:A288 G:A117, U:A118
4tp8 A1608 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1735, A1736, A1737 U:A571
4tp8 A1622 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1801, A1802, A1803 C:A1501, G:A1504 U:A1506
4tp8 A1627 2Bout A1825, A1826, A1827, A1828, A1829, A1830 G:A1385, G:A1386
4tp8 A1636 2Bout A1864, A1865, A1866, A1867, A1868, U101 G:A1525, G:A1526
4tp8 A1610 4Bout A1743, A1744, A1745, A1746, A1747, A1748 G:A646, U:A593, U:A594, G:A645
4tp8 A1619 Pout·2Bout A1788, A1789, A1790, A1791, E201, E202 G:A1079 U:A1076, G:A1077
4tp8 A1616 Pout·3Bout A1775, A1776, A1777, A1778, A1779, N201 A:A1360 C:A980, G:A1361, A:A1360
4tp8 A1623 Pout·3Bout A1804, A1805, A1806, A1807, A1808, A1809 G:A266 G:A257, G:A259, G:A258
4tp8 A1624 Pout·3Bout A1810, A1811, A1812, A1813, A1814, A1815 A:A781 U:A798, G:A799, G:A800
4tp8 A1632 Pout·3Bout A1846, A1847, A1848, A1849 A:A533 G:A515, U:A516, G:A517
4tp8 A1602 2Pout·Bout A1705, A1706, A1707, A1708, A1709, A1710 A:A329, A:A315 G:A319
4tp8 A1611 2Pout·2Bout A1749, A1750, A1751, A1752, A1753, A1754 U:A804, G:A803 G:A771, U:A772
4tp8 A1601 2Pout·2Bout A1701, A1702, A1703, A1704, T101, T102 G:A258, G:A259 G:A259, G:A260
4tp8 A1604 2Pout·4Bout A1715, A1716, A1717, A1718, A1719, A1720 G:A416, A:A415 G:A416, G:A417, U:A426, G:A425
4tp8 A1617 3Pout A1780, A1781, A1782, A1783, N202, N203 U:A1049, A:A1204, G:A1048
4tp8 A1640 5Pout·Rout A1881, A1882, A1883, A1884, A1885, A1886 C:A504, A:A523, C:A503, C:A536, G:A537 C:A522

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>