MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2288, See in JSmolClick on the image to toggle views Site type: 4Bout Schematic drawing for 4Bout List of all 105 Mg2+ binding sites with the site type 4Bout 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 4 of 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4ji5 A1714 4Bout A2010, A2011, A2012, A2013, A2014, A2015 G:A44, U:A45, G:A396, C:A395 4ji6 A1903 4Bout A3035, A3036, A3037, A3038, A3039, A3040 G:A44, U:A45, G:A396, C:A395 4ji7 A1831 4Bout A2500, A2501, A2502, A2503, A2504, A2505 G:A494, G:A491, G:A490, G:A492 4ji8 A1680 4Bout A2138, N201, N202, N203 A:A1360, G:A1361, C:A980, C:A979 4ji8 A1950 4Bout A3205, A3206, A3207, A3208, A3209, A3210 C:A43, G:A44, U:A45, G:A396 4nvv A3573 4Bout A4758, A4759, A4760, A4761, A4762 G:A2853, G:A2854, G:A2855, C:A2881 4nvx A3380 4Bout A4352, A4353, A4354, A4355 G:A2494, G:A2455, C:A2456, G:A2495 4nvz A3522 4Bout A4642, A4643, A4644, A4645, A4646, A4647 U:A2469, G:A2506, G:A2507, G:A2467 4nw1 A3412 4Bout A4444, A4445, A4446, A4447 G:A2843, G:A2844, G:A2845, C:A2871 4peb A3016 4Bout A3277, A3278, A3279, A3280, A3281, A3282 G:A1259, A:A1260, U:A580, U:A1258 4pec A3065 4Bout A3495, A3496, A3497, A3498, A3499, A3500 G:A2238, G:A2242, U:A2243, A:A2241 4pec A3020 4Bout A3296, A3297, A3298, A3299, A3300, A3301 G:A757, U:A755, A:A756, A:A739 4qcn A3552 4Bout A4852, A4853, A4854, A4855, A4856 G:A2854, G:A2855, C:A2881, G:A2853 4qcn A3503 4Bout A4690, A4691, A4692, A4693, A4694, A4695 U:A2469, G:A2506, G:A2507, G:A2467 4qcr A3380 4Bout A4270, A4271, A4272, A4273, A4274 A:A2253, G:A2250, G:A2254, U:A2097 4qcr A3575 4Bout A4873, A4874, A4875, A4876, A4877 G:A2854, G:A2855, C:A2881, G:A2853 4qct A3410 4Bout A4440, A4441, A4442, A4443, A4444 C:A2456, U:A2457, G:A2494, G:A2495 4qcz A3506 4Bout A4637, A4638, A4639, A4640, A4641, A4642 U:A2469, G:A2506, G:A2507, G:A2467 4qd1 A3422 4Bout A4347, A4348, A4349, A4350, A4351 C:A2456, U:A2457, G:A2494, G:A2495 4tol A1610 4Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A646, U:A593, U:A594, G:A645 4tov A3017 4Bout A3275, A3276, A3277, A3278, A3279, A3280 G:A1259, A:A1260, U:A580, U:A1258 4tp3 A3017 4Bout A3276, A3277, A3278, A3279, A3280, E303 U:A580, A:A1260, U:A1258, G:A1259 4tp3 A3021 4Bout A3298, A3299, A3300, A3301, A3302, A3303 U:A755, A:A756, A:A739, G:A757 4tp7 A3022 4Bout A3296, A3297, A3298, A3299, A3300, A3301 G:A757, A:A756, A:A739, U:A755 4tp7 A3096 4Bout A3630, A3631, A3632, A3633, A3634, A3635 G:A1464, G:A1445, C:A1446, G:A1465

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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