MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3464, See in JSmolClick on the image to toggle views Site type: 3Bout Schematic drawing for 3Bout List of all 341 Mg2+ binding sites with the site type 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 11 of 14 | « Previous | Next » | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4ji1 A1727 3Bout A2052, A2053, A2054, A2055, A2056, A2057 A:A101, G:A102, G:A64 4dr4 A1727 3Bout A2236, A2237, A2238, A2239 G:A490, G:A491, G:A494 4dr2 A1724 3Bout A2291, A2292, A2293, A2294 G:A490, G:A491, G:A494 3v26 A1718 3Bout A1977, A1978, A1979, A1980, A1981, A1982 G:A191, C:A187, U:A190 3v2e A1697 3Bout A2036, A2037, A2038, A2039, A2040 G:A126, G:A127, U:A125 3v22 A1696 3Bout A1904, A1905, A1906, A1907 G:A46, G:A394, C:A366 4dr6 A1684 3Bout A2201, A2202, A2203, A2204 G:A682, G:A683, A:A684 4ton A1641 3Bout A1885, A1886, A1887, A1888, U101, U102 G:A1525, G:A1526, C:A1509 4gas A1630 3Bout A1842, A1843, A1844, N201, N202, N203 C:A980, G:A1361, A:A1360 4gas A1623 3Bout A1808, A1809, A1810, A1811, A1812, A1813 G:A800, U:A798, G:A799 4gas A1620 3Bout A1791, A1792, A1793, A1794, A1795, A1796 U:A593, G:A645, G:A646 4tpe A1605 3Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A257, G:A258, G:A259 4dv7 A1602 3Bout A1901, A1902, A1903, A1904 C:A372, U:A375, G:A376 2i2p A1600 3Bout A1885, A1886, A1887, A1888, A1889 U:A1358, A:A1357, A:A1363 2qoy A1599 3Bout A2170, A2171, A2172, A2173, A2174, A2175 G:A1505, C:A1399, G:A1401 2i2u A1597 3Bout A1860, A1861, A1862, A1863, A1864 G:A1356, A:A1357, G:A1355 2qp0 A1591 3Bout A2118, A2119, A2120, A2121, E293, E1834 G:A11, U:A12, G:A22 2z4m A1591 3Bout A1836, A1837, A1838, A1839, A1840, A1841 G:A1525, G:A1526, C:A1524 2qbf A1590 3Bout A1838, A1839, A1840, A1841, A1842, A1843 C:A1509, G:A1525, G:A1526 3oaq A1570 3Bout A1747, A1748, A1749, A1750, A1751, U219 G:A1525, G:A1526, C:A1510 3ofo A1568 3Bout A1743, A1744, A1745, A1746, U216, U219 C:A1509, G:A1525, G:A1526 2z4k A1568 3Bout A1724, A1725, A1726, A1727, A1728, A1729 G:A377, G:A378, G:A376 2z4m A1567 3Bout A1715, A1716, A1717, A1718, A1719, A1720 G:A257, G:A258, G:A259 2qbj A1566 3Bout A1716, A1717, A1718, A1719, A1720, A1721 G:A257, G:A258, G:A259 2qbf A1566 3Bout A1716, A1717, A1718, A1719, A1720, A1721 G:A257, G:A258, G:A259

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/)
For any help please contact <dust@iwonka.med.virginia.edu>