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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 4tp0



4TP0 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to dalfopristin. this file contains the 30s subunit of the first 70s ribosome.
List of all 40 Mg2+ binding sites in the PDB structure 4tp0 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
4tp0 N201 4Pout A1781, A1782, A1783, A1784, N302, N303 U:A1049, C:A1203, A:A1204, G:A1048
4tp0 A1601 2Pout·Bout A1701, A1702, A1703, A1704, A1705, T101 G:A258, G:A259 G:A260
4tp0 A1602 2Pout·2Bout A1706, A1707, A1708, A1709, A1710, A1711 A:A329, A:A315 A:A320, G:A319
4tp0 A1603 Nb G:A362(N7) A1712, A1713, A1714, A1715, L201 G:A362 G:A361
4tp0 A1604 2Pout·4Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415, G:A416 G:A417, C:A418, U:A426, G:A416
4tp0 A1605 cis-2Oph A:A509(OP2), A:A510(OP2) A1722, A1723, A1724, A1725 G:A506, C:A507 A:A510
4tp0 A1606 Oph·Pout A:A547(OP1) A1726, A1727, A1728, A1729, A1730 G:A548 G:A402, C:A403
4tp0 A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 G:A566
4tp0 A1608 cis-2Oph A:A573(OP2), A:A574(OP2) A1736, A1737, A1738 U:A571 A:A574
4tp0 A1609 Oph·3Pout C:A578(OP1) A1739, A1740, A1741, A1742, A1743 C:A576, C:A817, U:A820 G:A575
4tp0 A1610 Pout·4Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A645 G:A646, U:A593, U:A594, G:A645
4tp0 A1611 2Pout·2Bout A1750, A1751, A1752, A1753, A1754, A1755 U:A804, G:A803 G:A771, U:A772
4tp0 A1612 Oph·3Pout A:A814(OP2) A1756, A1757, A1758, A1759, A1760 U:A904, A:A815, G:A577 A:A816
4tp0 A1613 Oph·2Pout U:A891(OP2) A1761, A1762, A1763, A1764, A1765 A:A892, G:A903 A:A906, U:A904, U:A905
4tp0 A1614 Oph·Pout C:A934(OP1) A1766, A1767, A1768, A1769, A1770 U:A1345
4tp0 A1615 Oph·Pout A:A937(OP2) A1771, A1772, A1773, A1774, A1775 A:A938 A:A938, G:A939
4tp0 A1616 Pout·3Bout A1776, A1777, A1778, A1779, A1780, N301 A:A1360 C:A980, G:A1361, A:A1360
4tp0 A1617 poly-nuclear Mg2+ site C:A1054(OP2), A:A1197(OP2) A1785, A1786, A1787, A1788 G:A1198 U:A1199, G:A1198
4tp0 A1618 Pout·2Bout A1789, A1790, A1791, A1792, A1793, E201 G:A1079 U:A1076, G:A1077
4tp0 A1619 cis-2Oph C:A1303(OP1), G:A1304(OP2) A1794, A1795, A1796, A1797 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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