MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3464, See in JSmolClick on the image to toggle views Site type: 3Bout Schematic drawing for 3Bout List of all 341 Mg2+ binding sites with the site type 3Bout 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 12 of 14 | « 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 3v23 A3460 3Bout A4491, A4492, A4493, A4494, A4495, A4496 A:A1412, G:A1413, G:A1414 2qbe B3464 3Bout B3988, B3989, B3990, B3991, B3992, B3993 G:B2549, G:B2550, G:B2557 3df2 B3464 3Bout B4465, B4466, B4467, B4468, B4469, B4470 G:B2549, G:B2550, G:B2557 3v2f A3479 3Bout A4788, A4789, A4790, A4791, A4792 G:A494, G:A495, G:A496 3v23 A3489 3Bout A4601, A4602, A4603, A4604, A4605, A4606 C:A1305, G:A1623, G:A1624 3v27 A3502 3Bout A4651, A4652, A4653, A4654, A4655 G:A495, G:A496, G:A494 3v29 A3504 3Bout A4411, A4412, A4413, A4414, A4415 G:A496, G:A495, G:A494 4dhc A3510 3Bout A4208, A4209, A4210, A4211, A4212 G:A1309, G:A1310, G:A1311 3v27 A3517 3Bout A4712, A4713, A4714, A4715, A4716, A4717 G:A271, C:A271, U:A271 4nvx A3522 3Bout A4628, A4629, A4630, A4631 G:A2624, G:A2625, G:A2777 4nvx A3561 3Bout A4721, A4722, A4723, A4724, A4725, A4726 G:A1423, G:A1424, G:A1425 4nvz A3569 3Bout A4760, A4761, A4762, A4763, A4764 G:A2853, G:A2854, C:A2881 3v23 A3576 3Bout A4872, A4873, A4874, A4875, A4876 G:A2625, G:A2624, G:A2777 4dha A3577 3Bout A4296, A4297, A4298, A4299, A4300 G:A520, G:A521, G:A522 3v2d A3578 3Bout A5343, A5344, A5345, A5346 G:A407, G:A406, U:A421 3v29 A3593 3Bout A4751, A4752, A4753, A4754, A4755, A4756 U:A350, G:A348, G:A349 4qcn A3598 3Bout A4985, A4986, A4987, A4988 G:A1355, G:A1356, G:A1357 3v23 A3603 3Bout A5012, A5013, A5014, A5015, A5016, A5017 G:A2009, G:A2010, U:A2011 3v27 A3607 3Bout A5104, A5105, A5106, A5107 G:A176, G:A177, G:A175 4qcr A3621 3Bout A5005, A5006, A5007, A5008 G:A1355, G:A1356, G:A1357 3v27 A3632 3Bout A5247, A5248, A5249, A5250, A5251, A5252 G:A315, C:A316, A:A314 3v27 A3636 3Bout A5266, A5267, A5268, A5269, A5270, A5271 G:A743, G:A744, G:A745 3v27 A3646 3Bout A5313, A5314, A5315, A5316, A5317, A5318 G:A1594, U:A1406, G:A1595 4nvz A3725 3Bout A5072, A5073, A5074, A5075 A:A847, G:A845, G:A846 4nvv A3731 3Bout A5070, A5071, A5072, A5073 G:A845, A:A847, G:A846

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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