MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoy:A1567, See in JSmolClick on the image to toggle views Site type: 2Bout Schematic drawing for 2Bout List of all 555 Mg2+ binding sites with the site type 2Bout 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 6 of 23 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qow A1592 2Bout A2126, A2127, A2128, A2129, A2130, A2131 G:A941, G:A942 2i2p A1592 2Bout A1843, A1844, A1845, A1846, A1847, A1848 U:A37, G:A38 2qou A1592 2Bout A2135, A2136, A2137, A2138, A2139, A2140 U:A37, G:A38 2qoy A1592 2Bout A2137, A2138, A2139, A2140, A2141, A2142 U:A37, G:A38 1vs7 A1592 2Bout A1838, A1839, A1840, A1841, A1842, A1843 G:A1525, G:A1526 1vs5 A1592 2Bout A1838, A1839, A1840, A1841, A1842, A1843 G:A38, U:A37 2qbh A1592 2Bout A1837, A1838, A1839, A1840, A1841, A1842 G:A38, U:A37 2z4k A1593 2Bout A1841, A1842, A1843, A1844, A1845, A1846 U:A37, G:A38 2qbj A1594 2Bout A1855, A1856, A1857, A1858, A1859, A1860 U:A37, G:A38 2qp0 A1594 2Bout A2134, A2135, A2136, A2137, A2138, A2139 G:A1385, G:A1386 2qbf A1594 2Bout A1858, A1859, A1860, A1861, A1862, A1863 G:A38, U:A37 2aw7 A1595 2Bout A1860, A1861, A1862, A1863, A1864, A1865 G:A38, U:A37 2z4m A1595 2Bout A1856, A1857, A1858, A1859, A1860, A1861 U:A37, G:A38 1vs7 A1596 2Bout A1858, A1859, A1860, A1861, A1862, A1863 G:A38, U:A37 2qou A1599 2Bout A2168, A2169, A2170, A2171, A2172, A2173 G:A1401, C:A1402 4dr6 A1602 2Bout A2003, A2004, A2005, A2006, A2007 G:A377, G:A376 4dr5 A1602 2Bout A1903, A1904, A1905, A1906, A1907 G:A377, G:A376 4ji1 A1605 2Bout A1907, A1908, A1909, A1910, A1911 G:A1526, G:A1525 4ji6 A1606 2Bout A2015, A2016, A2017, A2018, A2019 G:A1526, G:A1525 4ji7 A1608 2Bout A2114, A2115, A2116, A2117, A2118 G:A1526, G:A1525 4dv4 A1611 2Bout A1922, A1923, A1924, A1925 G:A1525, G:A1526 4ji4 A1611 2Bout A1922, A1923, A1924, A1925, A1926 G:A1526, G:A1525 4dr5 A1611 2Bout A1928, A1929, A1930, A1931, A1932 G:A1526, G:A1525 4dr6 A1611 2Bout A2028, A2029, A2030, A2031, A2032 G:A1525, G:A1526 4nxm A1612 2Bout A1922, A1923, A1924, A1925, A1926 G:A1526, G:A1525

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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