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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 4tpc



4TPC (2.8Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to flopristin and linopristin. this file contains the 30s subunit of the first 70s ribosome.
List of all 40 Mg2+ binding sites in the PDB structure 4tpc 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
4tpc A1601 2Pout·Bout A1701, A1702, A1703, A1704, A1705, T101 G:A258, G:A259 G:A260
4tpc A1602 2Pout·2Bout A1706, A1707, A1708, A1709, A1710, A1711 A:A329, A:A315 A:A320, G:A319
4tpc A1603 Nb G:A362(N7) A1712, A1713, A1714, A1715, L201 G:A361, G:A362 G:A361
4tpc A1604 2Pout·5Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415, G:A416 G:A416, G:A417, U:A426, C:A418, G:A425
4tpc A1605 cis-2Oph A:A509(OP2), A:A510(OP2) A1722, A1723, A1724, A1725 G:A506, C:A507 A:A510
4tpc A1606 Oph·Pout A:A547(OP1) A1726, A1727, A1728, A1729, A1730 G:A548 C:A403, G:A402
4tpc A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 G:A566
4tpc A1608 cis-2Oph A:A573(OP2), A:A574(OP2) A1736, A1737, A1738 U:A571
4tpc A1609 Oph·3Pout C:A578(OP1) A1739, A1740, A1741, A1742, A1743 C:A576, C:A817, U:A820 G:A575
4tpc A1610 5Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A646, C:A647, U:A593, G:A592, G:A645
4tpc A1611 2Pout·3Bout A1750, A1751, A1752, A1753, A1754, A1755 G:A803, U:A804 G:A771, U:A772, G:A773
4tpc A1612 Oph·2Pout A:A814(OP2) A1756, A1757, A1758, A1759, A1760 G:A577, A:A815
4tpc A1613 Oph·2Pout U:A891(OP2) A1761, A1762, A1763, A1764, A1765 A:A892, G:A903 A:A906, U:A904, U:A905
4tpc A1614 Oph·Pout C:A934(OP1) A1766, A1767, A1768, A1769, A1770 U:A1345
4tpc A1615 Oph A:A937(OP2) A1771, A1772, A1773, A1774, A1775 A:A938, G:A939
4tpc A1616 Pout·3Bout A1776, A1777, A1778, N201, N202, N203 A:A1360 G:A1361, C:A980, A:A1360
4tpc A1617 4Pout A1779, A1780, A1781, A1782, N204, N205 C:A1203, A:A1204, G:A1048, U:A1049
4tpc 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
4tpc A1619 Pout·2Bout A1787, A1788, A1789, A1790, A1791, A1792 G:A1079 U:A1076, G:A1077
4tpc A1620 cis-2Oph C:A1303(OP1), G:A1304(OP2) A1793, A1794, A1795, A1796 G:A1242 G:A1304, G:A1305

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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