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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 3v2d



3V2D (2.7Å) -- RIBOSOME : Crystal structure of yfia bound to the 70s ribosome. this pdb entry contains coordinates for the 50s subunit of the 1st ribosome in the asu
List of all 177 Mg2+ binding sites in the PDB structure 3v2d in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
Page 8 of 9 | | | 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
3v2d A3422 2Pout·Bout A4907, A4908, A4909, A4910, A4911 G:A2597, G:A1904 G:A2595
3v2d A3694 2Pout·Bout A5669, A5670, A5671, A5672, A5673 C:A2441, C:A2442 C:A2586
3v2d A3702 2Pout·Bout A5699, A5700, A5701, A5702 A:A2775, C:A2774 A:A2775
3v2d A3323 2Pout·2Bout A4599, A4600, A4601, A4602 A:A1634, G:A1627 G:A1628, U:A1629
3v2d A3306 2Pout·2Bout A4541, A4542, A4543, A4544, A4545 A:A1354, A:A1353 G:A1355, G:A1356
3v2d A3158 2Pout·3Bout A4126, A4127, A4128, A4129, A4130, A4131 A:A299, C:A336 A:A300, A:A299, G:A338
3v2d A3499 2Pout·3Bout A5123, A5124, A5125, A5126, A5127 A:A2005, G:A2004 G:A1650, G:A1651, G:A1649
3v2d A3554 2Pout·3Bout A5274, A5275, A5276, A5277, A5278, A5279 A:A2360, C:A2359 U:A2357, A:A2361, C:A2356
3v2d A3662 2Pout·4Bout A5548, A5549, A5550, A5551, A5552, A5553 C:A2452, A:A2453 A:A2453, A:A2497, G:A2454, G:A2455
3v2d A3670 2Pout·4Bout A5578, A5579, A5580, A5581, A5582 C:A834, A:A835 A:A835, G:A836, G:A942, U:A943
3v2d A3657 2Pout·2Rout·3Bout A5528, A5529, A5530, A5531, A5532 A:A1609, G:A1619 A:A1608, C:A1617 G:A1619, G:A1613, G:A1620
3v2d A3683 3Pout A5620, A5621, A5622, A5623, A5624 A:A866, U:A905, C:A865
3v2d A3250 3Pout·Rout A4382, A4383, A4384, A4385, A4386 C:A1990, G:A1989, G:A1667 G:A1667
3v2d A3172 3Pout·Bout A4173, A4174, A4175, A4176, P310 G:A831, G:A944, U:A568 A:A2448
3v2d A3149 3Pout·2Rout A4099, A4100, A4101, A4102, A4103 G:A690, A:A781, A:A782 U:A1777, G:A780
3v2d A3512 3Pout·Rout·Bout A5167, A5168, A5169, A5170, A5171 C:A698, G:A1555, C:A697 A:A1554 A:A1554
3v2d A3363 3Pout·2Bout A4701, A4702, A4703, A4704, A4705, A4706 G:A1332, C:A1333, U:A1313 U:A1335, G:A1334
3v2d A3693 3Pout·Rout·3Bout A5663, A5664, A5665, A5666, A5667, A5668 G:A570, A:A973, U:A569 G:A972 A:A820, A:A821, U:A568
3v2d A3402 3Pout·4Bout A4838, A4839, A4840, A4841, A4842, A4843 U:A29, A:A447, A:A28 G:A474, G:A473, U:A29, G:A30
3v2d A3223 4Pout·Bout A4312, A4313, A4314, A4315 C:A2745, U:A2746, U:A2754, C:A2755 G:A2747

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].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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