`

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

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 2qp1:B2994, See in JSmolMgRNA representative site for type OP-4PO         Click on the image to toggle views


Site type: Oph·4Pout

Schematic drawing for
Oph·4Pout

MgRNA type OP-4PO
List of all 231 Mg2+ binding sites with the site type Oph·4Pout 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 8 of 10 | | | 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
4gd2 A1617 Oph·4Pout A:A560(OP2) A1779, A1780, A1781, A1782, A1783 U:A562, A:A563, G:A557, G:A558 A:A559
4ji0 A1632 Oph·4Pout U:A560(OP1) A1956, A1957, A1958, A1959 A:A563, G:A557, G:A558, C:A562 A:A559
4ji3 A1632 Oph·4Pout U:A560(OP2) A1958, A1959, A1960, A1961 C:A562, A:A563, G:A557, G:A558 G:A566
4nvx A3310 Oph·4Pout G:A741(OP1) A4191, A4192, A4193, A4194 A:A1784, A:A1785, G:A2608, C:A1983 G:A2607
4nvz A3577 Oph·4Pout C:A31(OP1) A4785, A4786, A4787, A4788, A4789 G:A1285, U:A1244, C:A1245, U:A1286 A:A1259
4nvz A3420 Oph·4Pout G:A788(OP1) A4388, A4389, A4390, A4391, A4392 A:A1815, C:A2005, G:A2620, A:A1816 G:A2619
4nvz A3347 Oph·4Pout U:A2039(OP1) A4197, A4198, A4199, A4200, A4201 G:A2040, A:A2080, G:A600, A:A601
4nw1 A3305 Oph·4Pout G:A741(OP1) A4189, A4190, A4191, A4192 A:A1784, A:A1785, C:A1983, G:A2608 G:A2607
4pe9 A1607 Oph·4Pout A:A560(OP2) A1731, A1732, A1733, A1734, A1735 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
4pea A1617 Oph·4Pout A:A560(OP2) A1775, A1776, A1777, A1778, A1779 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
4pec A3120 Oph·4Pout U:A2243(OP1) A3736, A3737, A3738, A3739 C:A192, U:A193, C:A198, A:A199
4pec A3042 Oph·4Pout G:A1333(OP2) A3385, A3386, A3387, A3388, A3389 U:A1313, C:A1314, G:A1334, G:A1332 G:A1333, C:A1335
4qcn A3288 Oph·4Pout U:A1008(OP1) A4057, A4058, A4059, A4060, A4061 C:A1009, C:A2510, A:A2509, G:A992
4qcn A3559 Oph·4Pout C:A31(OP1) A4875, A4876, A4877, A4878, A4879 G:A1285, U:A1244, C:A1245, U:A1286 A:A1259
4qcn A3398 Oph·4Pout G:A788(OP1) A4383, A4384, A4385, A4386, A4387 A:A1815, A:A1816, G:A2620, C:A2005 G:A2619
4qcn A3541 Oph·4Pout G:A1859(OP1) A4815, A4816, A4817, A4818, A4819 G:A1803, A:A1994, A:A1804, G:A1995
4qcp A3328 Oph·4Pout G:A741(OP1) A4229, A4230, A4231, A4232 A:A1784, A:A1785, G:A2608, C:A1983 G:A2607
4qcp A3281 Oph·4Pout U:A2017(OP1) A4116, A4117, A4118, A4119, A4120 A:A578, G:A577, A:A2058, G:A2018
4qcp A3440 Oph·4Pout G:A1828(OP1) A4521, A4522, A4523, A4524, A4525 G:A1772, A:A1972, A:A1773, G:A1973
4qcr A3421 Oph·4Pout G:A788(OP1) A4404, A4405, A4406, A4407, A4408 A:A1815, A:A1816, G:A2620, C:A2005 G:A2619
4qcr A3564 Oph·4Pout G:A1859(OP1) A4837, A4838, A4839, A4840, A4841 G:A1803, A:A1994, A:A1804, G:A1995
4qct A3332 Oph·4Pout G:A741(OP1) A4231, A4232, A4233, A4234 A:A1784, A:A1785, G:A2608, C:A1983 G:A2607
4qct A3254 Oph·4Pout U:A963(OP1) A4032, A4033, A4034, A4035, A4036 C:A964, C:A2498, A:A2497, G:A947
4qct A3286 Oph·4Pout U:A2017(OP1) A4117, A4118, A4119, A4120, A4121 A:A578, G:A577, A:A2058, G:A2018
4qct A3447 Oph·4Pout G:A1828(OP1) A4533, A4534, A4535, A4536, A4537 G:A1772, A:A1972, A:A1773, G:A1973

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>