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 2 of 23 | « 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 1q82 A8063 2Bout A3691, A6490, A6914, A7234, A7312, A7362 G:A1364, G:A1363 1q86 A8063 2Bout A3708, A6520, A6952, A7265, A7342, A7393 G:A1364, G:A1363 1qvf 08063 2Bout 03692, 06481, 06905, 07215, 07288, 07339 G:01364, G:01363 1s72 08063 2Bout 03705, 06522, 06946, 07266, 07342, 07395 G:01364, G:01363 1vq4 08063 2Bout 04491, 07231, 07630, 07930, 08069, 08163 G:01364, G:01363 1vq5 08063 2Bout 04495, 07257, 07667, 07975, 08157 G:01364, G:01363 1vq6 08063 2Bout 04489, 07215, 07631, 07939, 08121, 08170 G:01364, G:01363 1vs5 A1592 2Bout A1838, A1839, A1840, A1841, A1842, A1843 G:A38, U:A37 1vs5 A1575 2Bout A1756, A1757, A1758, A1759, A1760, A1761 G:A1385, G:A1386 1vs5 A1588 2Bout A1818, A1819, A1820, A1821, A1822, A1823 G:A1526, G:A1525 1vs6 B2907 2Bout B3026, B3027, B3028, B3029, B3030, E202 U:B580, G:B1259 1vs6 B2961 2Bout B3284, B3285, B3286, B3287, B3288, B3289 G:B798, G:B797 1vs7 A1592 2Bout A1838, A1839, A1840, A1841, A1842, A1843 G:A1525, G:A1526 1vs7 A1596 2Bout A1858, A1859, A1860, A1861, A1862, A1863 G:A38, U:A37 1vs7 A1579 2Bout A1781, A1782, A1783, A1784, A1785, A1786 G:A1386, G:A1385 1vs7 A1572 2Bout A1746, A1747, A1748, A1749, A1750, P221 G:A377, G:A376 1vs7 A1558 2Bout A1671, A1672, A1673, A1674, A1675, A1676 G:A1050, G:A1207 1vs8 B2955 2Bout B3257, B3258, B3259, B3260, B3261, B3262 U:B434, A:B42 1vs8 B2963 2Bout B3300, B3301, B3302, B3303, B3304, B3305 G:B17, U:B18 1vs8 E202 2Bout B3156, E255, E256, E257, E258, E260 G:B798, G:B797 1vt2 A2930 2Bout A3167, A3168, A3169, A3170, E203, E204 G:A797, G:A798 1vt2 A2923 2Bout A3136, A3137, A3138, A3139, A3140, A3141 G:A638, G:A651 1vt2 A2905 2Bout A3038, A3039, A3040, A3041, A3042, A3043 U:A18, G:A17 1vt2 A2991 2Bout A3451, A3452, A3453, A3454, A3455, A3456 U:A842, G:A841 1y26 X104 2Bout X284, X285, X286, X287, X288, X289 G:X43, G:X44

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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