MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoz:B2982, See in JSmolClick on the image to toggle views Site type: Pout·3Bout Schematic drawing for Pout·3Bout List of all 341 Mg2+ binding sites with the site type Pout·3Bout in RNA crystal structures in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID" Page 4 of 14 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qbh A1563 Pout·3Bout A1699, A1700, A1701, A1702, A1703, A1704 A:A781 G:A800, G:A799, U:A798 2z4k A1564 Pout·3Bout A1700, A1701, A1702, A1703, A1704, A1705 A:A781 U:A798, G:A799, G:A800 2z4k A1565 Pout·3Bout A1706, A1707, A1708, A1709, A1710, A1711 A:A559 G:A9, A:A10, A:A559 2aw7 A1566 Pout·3Bout A1719, A1720, A1721, A1722, A1723, A1724 G:A266 G:A257, G:A258, G:A259 2qbf A1567 Pout·3Bout A1722, A1723, A1724, A1725, A1726, A1727 A:A781 G:A800, U:A798, G:A799 2aw7 A1567 Pout·3Bout A1725, A1726, A1727, A1728, A1729, A1730 A:A781 G:A800, U:A798, G:A799 1vs7 A1567 Pout·3Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259 2qbj A1567 Pout·3Bout A1722, A1723, A1724, A1725, A1726, A1727 A:A781 G:A800, U:A798, G:A799 1vs7 A1568 Pout·3Bout A1724, A1725, A1726, A1727, A1728, A1729 A:A781 U:A798, G:A800, G:A799 2z4m A1568 Pout·3Bout A1721, A1722, A1723, A1724, A1725, A1726 A:A781 G:A800, U:A798, G:A799 2qou A1574 Pout·3Bout A2052, A2053, A2054, A2055, A2056, A2057 G:A1385 G:A1385, G:A1386, C:A1384 2i2p A1575 Pout·3Bout A1765, A1766, A1767, A1768, A1769 U:A1348 G:A1370, G:A1371, U:A1372 2qow A1589 Pout·3Bout A2110, A2111, N280, N281, N1823, N1826 A:A1360 C:A980, G:A1361, A:A1360 2qp0 A1589 Pout·3Bout A2109, A2110, A2111, A2112, N279, N281 A:A1360 C:A980, A:A1360, G:A1361 2qbh A1599 Pout·3Bout A1871, A1872, A1873, A1874, A1875, A1876 C:A1400 C:A1399, G:A926, G:A1505 4ton A1605 Pout·3Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259 4gd2 A1605 Pout·3Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259 4tpa A1605 Pout·3Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259 4tow A1605 Pout·3Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259 4pea A1608 Pout·3Bout A1732, A1733, A1734, A1735, A1736, A1737 A:A315 G:A319, A:A320, G:A318 4tpa A1612 Pout·3Bout A1752, A1753, A1754, A1755, A1756, A1757 A:A415 G:A417, U:A426, G:A416 4tpc A1616 Pout·3Bout A1776, A1777, A1778, N201, N202, N203 A:A1360 G:A1361, C:A980, A:A1360 4pe9 A1616 Pout·3Bout A1776, A1777, A1778, N201, N202, N203 A:A1360 C:A980, G:A1361, A:A1360 4tp8 A1616 Pout·3Bout A1775, A1776, A1777, A1778, A1779, N201 A:A1360 C:A980, G:A1361, A:A1360 4tou A1616 Pout·3Bout A1776, A1777, A1778, N201, N202, N203 A:A1360 C:A980, G:A1361, A:A1360

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].

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