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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 2qan:A2016, See in JSmolMgRNA representative site for type 2PO-2BO        Click on the image to toggle views


Site type: 2Pout·2Bout

Schematic drawing for
2Pout·2Bout

MgRNA type 2PO-2BO
List of all 279 Mg2+ binding sites with the site type 2Pout·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 6 of 12 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v22 A1690 2Pout·2Bout A1878, A1879, A1880, A1881, A1882, A1883 G:A803, U:A804 U:A772, G:A771
3v23 A3365 2Pout·2Bout A4128, A4129, A4130, A4131, A4132 G:A430, A:A216 G:A352, U:A431
3v23 A3376 2Pout·2Bout A4176, A4177, A4178, A4179, A4180, A4181 G:A1627, A:A1634 U:A1629, G:A1628
3v23 A3375 2Pout·2Bout A4170, A4171, A4172, A4173, A4174, A4175 G:A1624, C:A698 A:A1634, G:A1626
3v23 A3542 2Pout·2Bout A4766, A4767, A4768, A4769 A:A233, G:A266 A:A233, C:A264
3v23 A3593 2Pout·2Bout A4952, A4953, A4954, A4955, A4956, A4957 G:A1891, C:A1892 G:A1846, G:A1845
3v23 A3369 2Pout·2Bout A4147, A4148, A4149, A4150, A4151 U:A1397, C:A1398 G:A1400, G:A1401
3v24 A1669 2Pout·2Bout A1808, A1809, A1810, A1811 G:A803, U:A804 G:A771, U:A772
3v25 A3303 2Pout·2Bout A3759, A3760, A3761, A3762, A3763 A:A1353, A:A1354 G:A1355, G:A1356
3v25 A3269 2Pout·2Bout A3627, A3628, A3629, A3630 A:A299, C:A336 A:A299, G:A338
3v26 A1696 2Pout·2Bout A1883, A1884, A1885, A1886, A1887, A1888 C:A536, A:A535 G:A537, G:A538
3v26 A1691 2Pout·2Bout A1856, A1857, A1858, A1859, A1860, A1861 A:A609, G:A610 G:A627, G:A628
3v26 A1723 2Pout·2Bout A2004, A2005, A2006, A2007, A2008, A2009 U:A813, G:A577 G:A577, G:A765
3v27 A3623 2Pout·2Bout A5195, A5196, A5197, A5198, A5199, A5200 G:A1630, G:A1633 C:A1631, G:A1630
3v27 A3422 2Pout·2Bout A4309, A4310, A4311, A4312, A4313, A4314 C:A698, G:A1624 G:A1626, A:A1634
3v27 A3601 2Pout·2Bout A5073, A5074, A5075, A5076, A5077, A5078 A:A1353, A:A1354 G:A1355, G:A1356
3v28 A1722 2Pout·2Bout A1920, A1921, A1922, A1923, A1924, A1925 C:A893, G:A894 G:A895, G:A894
3v29 A3422 2Pout·2Bout A4108, A4109, A4110, A4111, A4112, A4113 A:A1354, A:A1353 G:A1355, G:A1356
3v29 A3462 2Pout·2Bout A4262, A4263, A4264, A4265 A:A1494, A:A1495 G:A1492, A:A1496
3v29 A3353 2Pout·2Bout A3828, A3829, A3830, A3831 C:A336, A:A299 A:A300, G:A338
3v29 A3592 2Pout·2Bout A4746, A4747, A4748, A4749, A4750, R302 G:A2004, G:A1650 G:A1650, G:A1651
3v2c A1811 2Pout·2Bout A2334, A2335, A2336, A2337, A2338, A2339 U:A804, G:A803 U:A772, G:A771
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
3v2e A1690 2Pout·2Bout A2012, A2013, A2014, A2015, A2016 G:A265, G:A266 G:A258, G:A259

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/)
For any help please contact <dust@iwonka.med.virginia.edu>