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 5 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 2qan A2175 2Bout A2176, A2177, A2178, A2179, A2180, A2181 G:A376, G:A377 2qan A2312 2Bout A2313, A2314, A2315, A2316, A2317, A2318 U:A37, G:A38 2qan A2182 2Bout A2183, A2184, A2185, A2186, A2187, A2188 G:A941, G:A942 2qan A2107 2Bout A2109, A2110, A2111, A2112, E2108, E2113 U:A1076, G:A1077 2qao B3382 2Bout B3933, B3934, B3935, B3936, B3937, B3938 G:B1259, U:B580 2qao B3172 2Bout B3760, B3761, B3762, B3763, B3764, B3765 G:B798, G:B797 2qao B3389 2Bout B3939, B3940, B3941, B3942, B3943, B3944 G:B651, U:B652 2qb9 A2294 2Bout A2596, A2597, A2598, A2599, A2600, A2601 G:A38, U:A37 2qb9 A2219 2Bout A2535, A2536, A2537, A2538, A2539, A2540 G:A917, U:A916 2qb9 A2270 2Bout A2576, A2577, A2578, A2579, A2580, A2581 G:A1525, G:A1526 2qb9 A2157 2Bout A2484, A2485, A2486, A2487, A2488, A2489 G:A942, G:A941 2qb9 A2192 2Bout A2513, A2514, A2515, A2516, A2517, A2518 G:A1385, G:A1386 2qba B3331 2Bout B3881, B3882, B3883, E333, E334, E337 G:B798, G:B797 2qba B3246 2Bout B3812, B3813, B3814, B3815, B3816, B3817 G:B43, U:B434 2qba B3464 2Bout B3988, B3989, B3990, B3991, B3992, B3993 G:B2550, G:B2557 2qbb A2288 2Bout A2605, A2606, A2607, A2608, A2609, A2610 G:A1525, G:A1526 2qbb A2175 2Bout A2513, A2514, A2515, A2516, A2517, A2518 G:A376, G:A377 2qbb A2312 2Bout A2625, A2626, A2627, A2628, A2629, A2630 U:A37, G:A38 2qbb A2182 2Bout A2519, A2520, A2521, A2522, A2523, A2524 G:A941, G:A942 2qbc B3172 2Bout B3762, B3763, B3764, B3765, E202, E203 G:B797, G:B798 2qbc B3351 2Bout B3905, B3906, B3907, B3908, B3909 G:B2304, G:B2303 2qbc B3279 2Bout B3847, B3848, B3849, B3850, B3851, B3852 G:B2550, G:B2549 2qbd A2270 2Bout A2271, A2272, A2273, A2274, A2275, A2276 G:A1525, G:A1526 2qbd A2157 2Bout A2158, A2159, A2160, A2161, A2162, A2163 G:A941, G:A942 2qbd A2192 2Bout A2193, A2194, A2195, A2196, A2197, A2198 G:A1385, G:A1386

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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