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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 7 of 23 | | | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2otj 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03717, 03729, 07793, S8522 G:01676
2otj 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03804, 07759, 09047, 09788 A:0455, A:0460, A:0477 A:0455
2otj 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03898, 04044, 04187, 07856 G:0267, U:0268
2otl 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03644, 03969, 06187, 09397 G:01490, A:01487, U:01488 G:01489, G:01490
2otl 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03794, 07745, 09048, 09783 A:0455, A:0460, A:0477 A:0455
2otl 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03689, 03710, 03722, S8549 G:01676
2otl 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03883, 04027, 04174, 07843 G:0267, U:0268
2qal A2226 Oph·Ob G:A558(OP1) G:A299(O6) A2227, A2228, A2229, A2230 A:A560 G:A297 A:A298, A:A300, G:A566
2qal A2301 Oph·Ob A:A195(OP2) U:A180(O4) A2302, A2303, A2304, A2305 A:A179 C:A194 A:A181, A:A179
2qal A2237 Oph·Ob A:A533(OP1) U:A516(O4) A2238, A2239, A2240, A2241 A:A532 G:A515, G:A517
2qal A2259 Oph·Ob U:A1095(OP2) G:A1108(O6) A2260, A2261, A2262, A2263
2qam B3227 Oph·Ob A:B453(OP1) G:B450(O6) B3795, B3796, B3797, B3798 A:B449 A:B449
2qam B3516 Oph·Ob A:B1342(OP2) U:B1602(O4) B4031, B4032, B4033, B4034 G:B1601
2qam B3085 Oph·Ob C:B2248(OP2) U:B2249(O4) B3679, B3680, B3681, B3682 C:B2066, A:B2247
2qan A2278 Oph·Ob U:A1095(OP2) G:A1108(O6) A2279, A2280, A2281, A2282 C:A1096 G:A1094
2qan A2245 Oph·Ob G:A558(OP1) G:A299(O6) A2246, A2247, A2248, A2249 A:A560 G:A297 A:A298, A:A300, G:A566
2qan A2256 Oph·Ob A:A533(OP1) U:A516(O4) A2257, A2258, A2259, A2260 A:A532 G:A517, G:A515
2qan A2319 Oph·Ob A:A195(OP2) U:A180(O4) A2320, A2321, A2322, A2323 C:A194, A:A179 A:A181
2qao B3463 Oph·Ob C:B2248(OP2) U:B2249(O4) B3998, B3999, B4000, B4001 C:B2066, G:B2253 A:B2247
2qao B3370 Oph·Ob A:B453(OP1) G:B450(O6) B3923, B3924, B3925, B3926 A:B449
2qao B3532 Oph·Ob A:B1342(OP2) U:B1602(O4) B4050, B4051, B4052, B4053 G:B1601
2qb9 A2301 Oph·Ob A:A195(OP2) U:A180(O4) A2602, A2603, A2604, A2605 A:A179, C:A178 C:A194 A:A181, A:A179
2qb9 A2237 Oph·Ob A:A533(OP1) U:A516(O4) A2549, A2550, A2551, A2552 A:A532 G:A515, G:A517
2qb9 A2259 Oph·Ob U:A1095(OP2) G:A1108(O6) A2567, A2568, A2569, A2570
2qb9 A2226 Oph·Ob G:A558(OP1) G:A299(O6) A2541, A2542, A2543, A2544 A:A560 G:A297 A:A298, A:A300, G:A566

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>