MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbb:A2049, See in JSmolClick on the image to toggle views Site type: 2Pout·Bout Schematic drawing for 2Pout·Bout List of all 169 Mg2+ binding sites with the site type 2Pout·Bout 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 2 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qbh A1566 2Pout·Bout A1713, A1714, A1715, A1716, A1717, A1718 A:A1357, G:A1356 C:A1359 1vs5 A1566 2Pout·Bout A1711, A1712, A1713, A1714, A1715, A1716 A:A729, G:A727 G:A727 2z4k A1567 2Pout·Bout A1718, A1719, A1720, A1721, A1722, A1723 A:A1357, G:A1356 C:A1359 1vs7 A1570 2Pout·Bout A1734, A1735, A1736, A1737, A1738, A1739 C:A726, G:A727 G:A727 2qp0 A1580 2Pout·Bout A2065, A2066, A2067, A2068, A2069, A2070 G:A259, G:A258 G:A259 2i2u A1582 2Pout·Bout A1788, A1789, A1790, A1791, A1792, A1793 A:A1046, G:A1047 G:A1047 2z4k A1582 2Pout·Bout A1791, A1792, A1793, T233, T236 U:A323, G:A324 G:A324 2i2u A1586 2Pout·Bout A1811, A1812, A1813, A1814, A1815, A1816 G:A1356, A:A1357 C:A1359 4tpc A1601 2Pout·Bout A1701, A1702, A1703, A1704, A1705, T101 G:A258, G:A259 G:A260 4tou A1601 2Pout·Bout A1701, A1702, A1703, A1704, A1705, T101 G:A258, G:A259 G:A260 2qbf A1601 2Pout·Bout T358, A1892, A1893, A1894, A1895, A1896 G:A259, G:A258 G:A259 4tp0 A1601 2Pout·Bout A1701, A1702, A1703, A1704, A1705, T101 G:A258, G:A259 G:A260 4tp8 A1602 2Pout·Bout A1705, A1706, A1707, A1708, A1709, A1710 A:A329, A:A315 G:A319 4ji5 A1606 2Pout·Bout A1816, A1817, A1818, A1819, A1820 C:A620, A:A621 G:A617 4duy A1606 2Pout·Bout A1913, A1914, A1915, A1916 C:A651, G:A752 G:A752 4dv0 A1606 2Pout·Bout A1913, A1914, A1915, A1916 U:A652, C:A651 G:A752 4dv5 A1607 2Pout·Bout A1912, A1913, A1914, A1915 C:A651, U:A751 G:A752 4duz A1607 2Pout·Bout A1912, A1913, A1914, A1915 U:A652, C:A651 G:A752 4ji0 A1608 2Pout·Bout A1913, A1914, A1915, A1916 U:A751, U:A652 G:A752 4dr1 A1608 2Pout·Bout A1913, A1914, A1915, A1916 C:A651, U:A751 G:A752 4ji7 A1609 2Pout·Bout A2119, A2120, A2121, A2122, A2123 C:A620, A:A621 G:A617 4ji8 A1609 2Pout·Bout A2019, A2020, A2021, A2022, A2023 C:A620, A:A621 G:A617 4dr5 A1612 2Pout·Bout A1933, A1934, A1935, A1936, A1937 C:A620, A:A621 G:A617 4gaq A1623 2Pout·Bout A1807, A1808, A1809, A1810, A1811, K201 U:A798, A:A780 G:A799 4dr2 A1630 2Pout·Bout A2039, A2040, A2041, A2042, A2043 C:A620, G:A617 G:A617

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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