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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 2 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
1q81 A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3145, A3471, A5687, A8907 G:A1490, A:A1487 G:A1489, G:A1490
1q81 A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3388, A3524, A3665, A7343 G:A267, U:A268
1q81 A8004 Oph·Ob A:A459(OP1) G:A456(O6) A3295, A7245, A8569, A9293 A:A455, A:A460, A:A477 A:A455
1q82 A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3383, A3524, A3666, N8653 G:A267, U:A268
1q82 A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3145, A3468, A5657, A8914 G:A1490, A:A1487, U:A1488 G:A1490, G:A1489
1q86 A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3402, A3542, A3683, A7364 G:A267, U:A268
1q86 A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3158, A3488, A5693, A8920 G:A1490, A:A1487, U:A1488 G:A1489, G:A1490
1q86 A8004 Oph·Ob A:A459(OP1) G:A456(O6) A3310, A7266, A8569, A9299 A:A455, A:A460, A:A477 A:A455
1qvf 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03385, 03525, 03667, L8643 G:0267, U:0268
1qvg 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03137, 03457, 05612, 08918 G:01490, A:01487, U:01488 G:01489, G:01490
1qvg 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03374, 03510, 03652, L8645 G:0267, U:0268
1qvg 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03286, 07149, 08569, 09287 A:0455, A:0460, A:0477 A:0455
1s72 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03305, 07267, 08567, 09300 A:0455, A:0460, A:0477 A:0455
1s72 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03200, 03221, 03233, S8345 G:01676
1s72 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03154, 03479, 05700, 08915 G:01490, A:01487, U:01488 G:01489, G:01490
1s72 08027 Oph·Ob C:0240(OP1) G:0269(O6) 03393, 03538, 03680, 07365 G:0267, U:0268
1vq4 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03093, 04087, 07931, 09367 A:0477, A:0455, A:0460 A:0455
1vq4 08027 Oph·Ob C:0240(OP1) G:0269(O6) 04178, 04322, 04466, 08135 G:0267, U:0268
1vq4 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03983, 04004, 04015, 07965 G:01676
1vq4 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03937, 04264, 09715 G:01490, A:01487 G:01489, G:01490
1vq5 08062 Oph·Ob G:01489(OP2) G:01491(O6) 03948, 04271, 06452, 09720 G:01490, A:01487 G:01490, G:01489
1vq5 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03100, 04097, 07976, 09369 A:0477, A:0455, A:0460 A:0455
1vq5 08027 Oph·Ob C:0240(OP1) G:0269(O6) 04186, 04328, 04469, 08180 G:0267, U:0268
1vq5 08028 Oph·Ob A:01448(OP2) U:01677(O4) 03993, 04013, 04025, 08095 G:01676
1vq6 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03092, 04089, 07940, 09369 A:0477, A:0455, A:0460 A:0455

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>