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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 4pea



4PEA (2.95Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to quinupristin. this file contains the 30s subunit of the second 70s ribosome.
List of all 36 Mg2+ binding sites in the PDB structure 4pea 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
4pea A1607 Oph·Ob G:A558(OP1) G:A299(O6) A1728, A1729, A1730, A1731 A:A560 G:A297 A:A298, G:A566
4pea A1614 Oph·Ob A:A533(OP1) U:A516(O4) A1760, A1761, A1762, A1763 G:A515, G:A517
4pea A1613 cis-2Oph A:A509(OP2), A:A510(OP2) A1756, A1757, A1758, A1759 G:A506, C:A507 U:A508 A:A510
4pea A1641 2Bout A1884, A1885, A1886, A1887, A1888, U101 G:A1525, G:A1526
4pea A1637 2Bout A1867, A1868, A1869, A1870, A1871, A1872 G:A1386, G:A1385
4pea A1623 Pout·3Bout A1805, A1806, A1807, A1808, A1809, A1810 A:A781 U:A798, G:A799, G:A800
4pea A1630 Pout·3Bout A1839, A1840, A1841, A1842, N201, N202 A:A1360 A:A1360, C:A979, C:A980
4pea A1608 Pout·3Bout A1732, A1733, A1734, A1735, A1736, A1737 A:A315 G:A319, A:A320, G:A318
4pea A1620 Pout·4Bout A1788, A1789, A1790, A1791, A1792, A1793 G:A645 G:A645, G:A646, G:A592, U:A593
4pea A1605 Pout·4Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259, C:A267
4pea A1622 2Pout·3Bout A1799, A1800, A1801, A1802, A1803, A1804 G:A803, U:A804 G:A771, U:A772, G:A773
4pea A1606 2Pout·3Bout A1724, A1725, A1726, A1727, T101, T102 G:A258, G:A259 G:A258, G:A259, G:A260
4pea A1612 2Pout·4Bout A1750, A1751, A1752, A1753, A1754, A1755 G:A416, A:A415 G:A417, G:A425, U:A426, G:A416
4pea A1631 3Pout A1843, A1844, A1845, A1846, A1847, N203 U:A1049, A:A1204, G:A1048
4pea A1636 3Pout·Bout A1863, A1864, A1865, A1866 C:A1303, G:A1304, G:A1305 G:A1305
4pea A1615 5Pout·Rout A1764, A1765, A1766, A1767, A1768, A1769 C:A504, A:A523, C:A536, G:A537, C:A503 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/)
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