MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4m:A1592, See in JSmolClick on the image to toggle views Site type: Pout Schematic drawing for Pout List of all 94 Mg2+ binding sites with the site type Pout 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 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2bx2 L1511 Pout L2021, L2022, L2032, L2033, R2002, R2003 U:R12 3oar A1552 Pout A1660, A1661, A1662, A1663, A1664, A1665 G:A1079 2qou A1565 Pout A2005, A2006, A2007, A2008, A2009, A2010 U:A854 2z4m A1592 Pout A1842, A1843, A1844, A1845, A1846, A1847 A:A553 2qoy A1600 Pout A2176, A2177, A2178, A2179, A2180, A2181 G:A258 4dr6 A1628 Pout A2074, A2075, A2076, A2077, A2693 G:A21 4dv1 A1635 Pout A1971, A1972, A1973, A1974 U:A646 4dr4 A1648 Pout A2070, A2071, A2072, A2073 U:A20 3v22 A1686 Pout A1861, A1862, A1863, A1864, A1865, A1866 C:A770 4dr2 A1689 Pout A2199, A2200, A2201, A2202 G:A1079 3v26 A1695 Pout A1877, A1878, A1879, A1880, A1881, A1882 C:A770 4dr5 A1698 Pout A2134, A2135, A2136, A2137 C:A701 4ji3 A1700 Pout A2072, A2073, A2074, A2123 A:A1204 4dr2 A1725 Pout A2295, A2296, A2297, A2298 G:A371 4dr2 A1727 Pout A2303, A2304, A2305, A2306 G:A475 4dr4 A1728 Pout A2240, A2241, A2242, A2243 G:A371 3v26 A1733 Pout A2047, A2048, A2049, A2050, A2051 G:A1079 4dr2 A1733 Pout A2320, A2321, A2322, A2323 A:A448 3v28 A1750 Pout A2012, A2013, A2014, A2015, A2016 G:A1421 4dr2 A1775 Pout A2468, A2469, A2470, A2471 C:A882 4ji1 A1790 Pout A2432, A2433, A2434, A2435, A2436, A2437 U:A5 4lfb A1821 Pout A1915, A1916, A1917, A1918, A1919, A1920 C:A442 4dv6 A1841 Pout J301, J302, J303, N202, N203 C:A1189 4dr4 A1944 Pout A2415, A2416, A2417, A2418 U:A294 3df3 A2134 Pout A4135, A4136, A4137, A4138, A4139, A4140 U:A1205

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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