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 10 of 23 | « 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 4dv2 A1831 2Bout A2248, A2249, A2250, A2251 U:A125, G:A126 4dr5 A1832 2Bout A2381, A2382, A2383, A2384, A2385, A2386 G:A1385, G:A1386 4dv7 A1832 2Bout A2128, A2129, A2130, A2131 G:A1185, G:A1186 4duy A1836 2Bout A2307, A2308, A2309, A2310, A2311 G:A709, G:A710 4dv7 A1841 2Bout A2176, A2177, A2178, A2179, A2180 G:A1386, G:A1385 4ji6 A1842 2Bout A2675, A2676, A2677, A2678, A2679, A2680 G:A1385, G:A1386 4ji7 A1896 2Bout A2892, A2893, A2894, A2895, A2896, A2897 G:A1385, G:A1386 4dr4 A1945 2Bout A2419, A2420, A2421, A2422 G:A638, G:A639 4ji7 A2007 2Bout A3547, A3548, A3549, A3550, A3551, A3552 G:A376, G:A377 2qan A2107 2Bout A2109, A2110, A2111, A2112, E2108, E2113 U:A1076, G:A1077 2qal A2157 2Bout A2158, A2159, A2160, A2161, A2162, A2163 G:A941, G:A942 3df1 A2157 2Bout A4158, A4159, A4160, A4161, A4162, A4163 G:A941, G:A942 2qbd A2157 2Bout A2158, A2159, A2160, A2161, A2162, A2163 G:A941, G:A942 2qb9 A2157 2Bout A2484, A2485, A2486, A2487, A2488, A2489 G:A942, G:A941 2qbb A2175 2Bout A2513, A2514, A2515, A2516, A2517, A2518 G:A376, G:A377 3df3 A2175 2Bout A4176, A4177, A4178, A4179, A4180, A4181 G:A376, G:A377 2qan A2175 2Bout A2176, A2177, A2178, A2179, A2180, A2181 G:A376, G:A377 2qbb A2182 2Bout A2519, A2520, A2521, A2522, A2523, A2524 G:A941, G:A942 2qan A2182 2Bout A2183, A2184, A2185, A2186, A2187, A2188 G:A941, G:A942 3df3 A2182 2Bout A4183, A4184, A4185, A4186, A4187, A4188 G:A941, G:A942 3df1 A2192 2Bout A4193, A4194, A4195, A4196, A4197, A4198 G:A1385, G:A1386 2qbd A2192 2Bout A2193, A2194, A2195, A2196, A2197, A2198 G:A1385, G:A1386 2qb9 A2192 2Bout A2513, A2514, A2515, A2516, A2517, A2518 G:A1385, G:A1386 2qal A2192 2Bout A2193, A2194, A2195, A2196, A2197, A2198 G:A1385, G:A1386 3df3 A2218 2Bout A4219, A4220, A4221, A4222, A4223, A4224 G:A1386, G:A1385

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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