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

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Representative site 1egk:C14, See in JSmolMgRNA representative site for type BO             Click on the image to toggle views


Site type: Bout

Schematic drawing for
Bout

MgRNA type BO
List of all 132 Mg2+ binding sites with the site type Bout 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 5 of 6 | | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4ji1 A1805 Bout A2521, A2522, A2523, A2524, A2525, A2526 G:A587
4ji2 A1647 Bout A1989, A1990, Q301, Q302 G:A587
4ji2 A1702 Bout A2068, A2069, A2070, A2071 G:A700
4ji3 A1611 Bout A1922, A1923, A1924, A1925, A1926 G:A1525
4ji3 A1699 Bout A2068, A2069, A2070, A2071 G:A700
4ji6 A1791 Bout A2373, A2374, A2375, A2376, A2377, A2378 G:A926
4ji7 A1915 Bout A2999, A3000, A3001, A3002, A3003, A3004 U:A129
4nvx A3359 Bout A4307, A4308, A4309, A4310 G:A2000
4nw1 A3353 Bout A4306, A4307, A4308, A4309 G:A2000
4nxm A1703 Bout A2072, A2073, A2074, A2075 G:A700
4nxn A1626 Bout A1957, A1958, E301, E302 G:A21
4qcn A3472 Bout A4587, A4588, A4589, A4590, A4591 G:A2022
4qcn A3555 Bout A4860, A4861, A4862, A4863, 03104 G:A2292
4qcp A3383 Bout A4369, A4370, A4371, A4372, A4373 G:A2000
4qcp A3451 Bout A4547, A4548, A4549, A4550, A4551 G:A2280
4qcr A3496 Bout A4607, A4608, A4609, A4610, A4611 G:A2022
4qcr A3570 Bout A4857, A4858, A4859, A4860, A4861 G:A2387
4qct A3387 Bout A4376, A4377, A4378, A4379, A4380 G:A2000
4qct A3458 Bout A4557, A4558, A4559, A4560, A4561 G:A2280
4qcv A3523 Bout A4653, A4654, A4655, A4656, A4657 G:A2387
4qcv A3665 Bout A4905, A4906, A4907, A4908, F405, F406 G:A845
4qcx A3387 Bout A4309, A4310, A4311, A4312, A4313 G:A2000
4qcx A3468 Bout A4466, A4467, A4468, A4469 G:A2595
4qcz A3477 Bout A4551, A4552, A4553, A4554, A4555 G:A2022
4qcz A3562 Bout A4799, A4800, A4801, A4802 C:A2293

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>