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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qbd:A2237, See in JSmolMgRNA representative site for type OP-OB Click on the image to toggle views


Site type: Oph·Ob

Schematic drawing for
Oph·Ob
MgRNA type OP-OB
List of all 554 Mg2+ binding sites with the site type Oph·Ob 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 23 | | | 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
1w2b 03918 Oph·Ob A:0459(OP1) G:0456(O6) 04323, 04336, 04341, 04387 A:0460, A:0477 A:0455
1yhq 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03279, 04278, 08278, 09545 A:0477, A:0455, A:0460 A:0455
1yhq 08020 Oph·Ob C:0240(OP1) G:0269(O6) 04367, 04508, 04648, 08373 G:0267, U:0268
1yhq 08021 Oph·Ob A:01448(OP2) U:01677(O4) 04175, 04196, 04207, S8993 G:01676
1yi2 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03630, 03955, 06157, 09397 G:01490, A:01487, U:01488 G:01490, G:01489
1yi2 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03870, 04011, 04151, 07820 G:0267, U:0268
1yi2 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03675, 03696, 03708, S8549 G:01676
1yi2 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03780, 07722, 09045, 09781 A:0455, A:0460, A:0477 A:0455
1yij 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03884, 04027, 04171, 07833 G:0267, U:0268
1yij 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03793, 07734, 09046, 09782 A:0455, A:0460, A:0477 A:0455
1yij 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03687, 03708, 03720, S8549 G:01676
1yj9 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03690, 03830, 03977, M8946 G:0267, U:0268
1yj9 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03447, 03775, 09215 A:01487 G:01489, G:01490
1yj9 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03493, 03514, 03525, S8545 G:01676
1yjn 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03798, 07746, 09048, 09785 A:0455, A:0460, A:0477 A:0455
1yjn 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03691, 03712, 03724, 07782 G:01676
1yjn 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03891, 04031, 04172, 07846 G:0267, U:0268
1yjn 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03644, 03975, 06187, 09399 G:01490, A:01487, U:01488 G:01490
1yjw 78027 Oph·Ob C:0240(OP1) G:0269(O6) 04761, 04763, 04822, 04823 G:0267, U:0268
1yjw 78028 Oph·Ob A:01448(OP2) U:01677(O4) 07211, 07214, 07573, S4022 G:01676
1yjw 78062 Oph·Ob G:01489(OP2) G:01491(O6) 07298, 07300, 07304, 07305 A:01487, U:01488, G:01490 G:01490, G:01489
1yjw 78004 Oph·Ob A:0459(OP1) G:0456(O6) 05092, 05093, 05096, 05106 A:0455, A:0460, A:0477 A:0455
2avy A1579 Oph·Ob G:A558(OP1) G:A299(O6) A1778, A1779, A1780, A1781 A:A560 A:A298, G:A566
2avy A1592 Oph·Ob A:A195(OP2) U:A180(O4) A1840, A1841, A1842, A1843 C:A194, A:A179 A:A181, A:A179
2avy A1581 Oph·Ob A:A533(OP1) U:A516(O4) A1787, A1788, A1789, A1790 A:A532 G:A515, G:A517

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>