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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 4pe9



4PE9 (2.95Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to quinupristin. this file contains the 30s subunit of the first 70s ribosome.
List of all 38 Mg2+ binding sites in the PDB structure 4pe9 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
4pe9 A1601 2Pout·2Bout A1701, A1702, A1703, A1704, A1705, T101 G:A258, G:A259 G:A260, G:A259
4pe9 A1602 2Pout·2Bout A1706, A1707, A1708, A1709, A1710, A1711 A:A329, A:A315 G:A318, G:A319
4pe9 A1603 Nb G:A362(N7) A1712, A1713, A1714, A1715, L201 G:A361 G:A361
4pe9 A1604 Pout·5Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415 G:A416, U:A427, G:A417, C:A418, G:A425
4pe9 A1605 cis-2Oph A:A509(OP2), A:A510(OP2) A1722, A1723, A1724, A1725 G:A506, C:A507 A:A510
4pe9 A1606 Oph·Pout A:A547(OP1) A1726, A1727, A1728, A1729, A1730 G:A548 G:A402
4pe9 A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
4pe9 A1609 Oph·3Pout C:A578(OP1) A1739, A1740, A1741, A1742, A1743 C:A576, C:A817, U:A820 G:A575, G:A821
4pe9 A1610 5Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A646, U:A593, U:A594, U:A644, G:A645
4pe9 A1611 Pout·2Bout A1750, A1751, A1752, A1753, A1754, A1755 G:A803 G:A771, U:A772
4pe9 A1612 Oph·2Pout A:A814(OP2) A1756, A1757, A1758, A1759, A1760 G:A577, A:A815 A:A816
4pe9 A1613 Oph·2Pout U:A891(OP2) A1761, A1762, A1763, A1764, A1765 A:A892, G:A903 A:A906, U:A904, U:A905
4pe9 A1614 Oph·Pout C:A934(OP1) A1766, A1767, A1768, A1769, A1770 U:A1345 U:A1345
4pe9 A1615 Oph A:A937(OP2) A1771, A1772, A1773, A1774, A1775 A:A938, G:A939
4pe9 A1616 Pout·3Bout A1776, A1777, A1778, N201, N202, N203 A:A1360 C:A980, G:A1361, A:A1360
4pe9 A1617 4Pout A1779, A1780, A1781, A1782, N204, N205 U:A1049, C:A1203, A:A1204, G:A1048
4pe9 A1618 poly-nuclear Mg2+ site C:A1054(OP2), A:A1197(OP2) A1783, A1784, A1785, A1786 G:A1198 G:A1053 G:A1198, U:A1199, A:A1197
4pe9 A1619 Pout·2Bout A1787, A1788, A1789, A1790, A1791, A1792 G:A1079 U:A1076, G:A1077
4pe9 A1620 cis-2Oph C:A1303(OP1), G:A1304(OP2) A1793, A1794, A1795, A1796 G:A1242 G:A1305
4pe9 A1621 Ob G:A1417(O6) A1797, A1798, A1799, A1800, A1801 G:A1416, G:A1415 G:A1416

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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