MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbe:B3457, See in JSmolClick on the image to toggle views Site type: 2Pout·4Bout Schematic drawing for 2Pout·4Bout List of all 68 Mg2+ binding sites with the site type 2Pout·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 1 of 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3cc2 08071 2Pout·4Bout 03670, 05625, 06994, 07126, 07398, 07399 A:01815, C:01816 A:01759, U:01813, C:01818, U:01817 2otj 08071 2Pout·4Bout 04142, 06085, 07434, 07562, 07831, 07832 A:01815, C:01816 A:01759, U:01813, C:01818, U:01817 3v2d A3670 2Pout·4Bout A5578, A5579, A5580, A5581, A5582 C:A834, A:A835 A:A835, G:A836, G:A942, U:A943 3v2d A3662 2Pout·4Bout A5548, A5549, A5550, A5551, A5552, A5553 C:A2452, A:A2453 A:A2453, A:A2497, G:A2454, G:A2455 3v27 A3613 2Pout·4Bout A5135, A5136, A5137, A5138, A5139, A5140 G:A2846, G:A2845 G:A2845, G:A2846, U:A2847, G:A2848 3v29 A3578 2Pout·4Bout A4691, A4692, A4693, A4694, A4695, A4696 G:A2845, G:A2846 U:A2847, G:A2848, G:A2845, G:A2846 3v27 A3527 2Pout·4Bout A4764, A4765, A4766, A4767, A4768 A:A1701, A:A1700 G:A1699, G:A1702, G:A1703, G:A1763 4qcz A3471 2Pout·4Bout A4534, A4535, A4536, A4537, A4538 G:A2855, G:A2856 U:A2857, G:A2858, G:A2855, G:A2856 4qcn A3466 2Pout·4Bout A4569, A4570, A4571, A4572, A4573 G:A2855, G:A2856 U:A2857, G:A2858, G:A2855, G:A2856 3v27 A3461 2Pout·4Bout A4475, A4476, A4477, A4478, A4479, A4480 C:A2452, A:A2453 A:A2453, G:A2455, A:A2497, G:A2454 2qba B3457 2Pout·4Bout B3982, B3983, B3984, B3985, B3986, B3987 A:B2451, C:B2452 A:B2453, G:B2454, A:B2497, G:B2455 2qbe B3457 2Pout·4Bout B3982, B3983, B3984, B3985, B3986, B3987 A:B2451, C:B2452 A:B2497, G:B2455, A:B2453, G:B2454 2qam B3457 2Pout·4Bout B3985, B3986, B3987, B3988, B3989, B3990 A:B2451, C:B2452 A:B2497, G:B2455, A:B2453, G:B2454 4qcv A3444 2Pout·4Bout A4471, A4472, A4473, A4474, A4475, A4476 C:A2464, A:A2465 A:A2465, A:A2509, G:A2466, G:A2467 3v25 A3420 2Pout·4Bout A4152, A4153, A4154, A4155, A4156, A4157 G:A2845, G:A2846 G:A2848, G:A2845, G:A2846, U:A2847 4dhc A3418 2Pout·4Bout A3917, A3918, A3919, A3920, A3921 C:A2452, A:A2453 A:A2453, G:A2454, G:A2455, A:A2497 4qd1 A3390 2Pout·4Bout A4277, A4278, A4279, A4280, A4281, A4282 C:A2452, A:A2453 A:A2453, A:A2497, G:A2454, G:A2455 4qcp A3379 2Pout·4Bout A4357, A4358, A4359, A4360, A4361 G:A2845, G:A2846 U:A2847, G:A2848, G:A2845, G:A2846 4qct A3379 2Pout·4Bout A4354, A4355, A4356, A4357, A4358, A4359 C:A2452, A:A2453 A:A2453, A:A2497, G:A2454, G:A2455 4qcp A3374 2Pout·4Bout A4345, A4346, A4347, A4348, A4349, A4350 C:A2452, A:A2453 A:A2453, G:A2455, A:A2497, G:A2454 3v2f A3260 2Pout·4Bout A4130, A4131, A4132, A4133, A4134 U:A29, A:A447 G:A474, U:A29, G:A30, G:A473 3v2f A3214 2Pout·4Bout A3972, A3973, A3974, A3975, A3976, A3977 C:A2452, A:A2453 A:A2453, G:A2454, G:A2455, A:A2497 2qao B3152 2Pout·4Bout B3743, B3744, B3745, B3746, B3747, B3748 A:B2453, C:B2452 A:B2453, G:B2454, A:B2497, G:B2455 2qbc B3152 2Pout·4Bout B3745, B3746, B3747, B3748, B3749, B3750 C:B2452, A:B2453 A:B2453, G:B2454, A:B2497, G:B2455 4tp7 A3072 2Pout·4Bout A3519, A3520, A3521, A3522, A3523, A3524 A:A2453, C:A2452 A:A2497, A:A2453, G:A2454, G:A2455

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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