MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs8:B2932, See in JSmolClick on the image to toggle views Site type: 3Pout Schematic drawing for 3Pout List of all 207 Mg2+ binding sites with the site type 3Pout 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 9 | « 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 4duy A1837 3Pout A2312, A2313, A2314, A2315, A2316, A2317 U:A1345, C:A934, A:A1346 4dv1 A1611 3Pout A1923, A1924, A1925, A1926, A1927 G:A617, C:A620, A:A621 4dv2 A1638 3Pout A1977, A1978, A1979, A1980 U:A820, C:A578, G:A576 4dv4 A1786 3Pout A2122, A2123, A2124, A2125 A:A151, C:A150, G:A168 4dv4 A1607 3Pout A1913, A1914, A1915, A1916 U:A652, C:A651, G:A752 4dv6 A1848 3Pout A2326, A2327, A2328, A2329, A2330 U:A1345, C:A934, A:A1346 4dv6 A1606 3Pout A1913, A1914, A1915, A1916 U:A751, C:A651, U:A652 4dv7 A1607 3Pout A1912, A1913, A1914, A1915 C:A651, U:A652, U:A751 4dv7 A1785 3Pout A2100, A2101, A2102, A2103, A2104, A2105 C:A1103, A:A1101, C:A1100 4gar A3010 3Pout A3251, A3252, A3253, A3254, A3255, A3256 C:A560, G:A2038, A:A1008 4gar A3012 3Pout A3262, A3263, A3264, A3265, A3266, L301 G:A831, C:A944, U:A832 4gar A3074 3Pout A3550, A3551, A3552, A3553 A:A2711, G:A2714, C:A2710 4gas A1631 3Pout A1845, A1846, A1847, A1848, A1896, N204 U:A1049, A:A1204, G:A1048 4gau A3011 3Pout A3249, A3250, A3251, A3252, A3253, A3254 G:A559, C:A560, A:A1008 4gau A3027 3Pout A3337, A3338, A3339, A3340, A3341, A3342 G:A822, C:A965, A:A947 4gd1 A1617 3Pout A1781, A1782, A1783, A1784, N203, N204 G:A1048, A:A1204, U:A1049 4ji1 A1746 3Pout A2165, A2166, A2167, A2168, A2169, A2170 G:A800, U:A801, G:A778 4ji1 A1757 3Pout A2231, A2232, A2233, A2234, A2235, A2236 G:A588, C:A589, G:A644 4ji2 A1640 3Pout A1978, A1979, A1980, A1981 C:A578, G:A576, U:A820 4ji4 A1612 3Pout A1927, A1928, A1929, A1930, A1931 G:A617, C:A620, A:A621 4ji4 A1608 3Pout A1913, A1914, A1915, A1916 U:A652, C:A651, U:A751 4ji5 A1624 3Pout A1844, A1845, A1846, A1847 A:A16, G:A15, U:A14 4ji5 A1603 3Pout A1805, A1806, A1807, A1808 U:A652, C:A651, U:A751 4ji6 A1637 3Pout A2076, A2077, A2078, A2079 A:A16, U:A13, U:A14 4ji6 A1603 3Pout A2009, A2010, A2011, A2012 U:A652, C:A651, U:A751

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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