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

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Representative site 3df2:B3428, See in JSmolMgRNA representative site for type OP-OR          Click on the image to toggle views


Site type: Oph·Or

Schematic drawing for
Oph·Or

MgRNA type OP-OR
List of all 49 Mg2+ binding sites with the site type Oph·Or 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1kd1 A8093 Oph·Or G:A1071(OP1) A:A1070(O2') A3646, A3678, A3718, A9674 G:A627 A:A914, A:A913, G:A1071
1kqs 08014 Oph·Or G:02537(OP2) G:02102(O5') 03167, 03669, 07238, 08554 G:02102 C:02536, A:02101 G:02480, G:02481, A:02101
1m1k A8093 Oph·Or G:A1071(OP1) A:A1070(O2') A3244, A3276, A3318, A9277 G:A627 A:A914, A:A913, G:A1071
1vq4 08014 Oph·Or G:02537(OP2) G:02102(O5') 03964, 04474, 07922, 09353 G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
1vq6 08014 Oph·Or G:02537(OP2) G:02102(O5') 03967, 04472, 07931, 09355 G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
1vs6 B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3364, B3365, B3366, B3367 G:B2061 A:B2060 A:B2060, G:B2446
1vvz A1640 Oph·Or U:A1376(OP2) ARG:G94(NH1)
1yij 08014 Oph·Or G:02537(OP2) G:02102(O5') 03668, 04179, 07725, 09032 G:02102, G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
1yjn 08014 Oph·Or G:02537(OP2) G:02102(O5') 03672, 04180, 07737, 09033 G:02102, G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
1yjw 78014 Oph·Or G:02537(OP2) G:02102(O5') 08468, 09071, 09188, 09190 G:02102, G:02481 A:02101, C:02536 A:02101, G:02480, G:02481
2aw4 B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3360, B3361, B3362, B3363 G:B2061 A:B2060 A:B2060, G:B2446
2awb B3005 Oph·Or U:B1379(OP2) A:B1378(O2') B3475, B3476, B3477 G:B1380 G:B1380
2i2p A1585 Oph·Or G:A1068(OP1) G:A1387(O2') A1810, A1811, A1812, A1813 G:A1094
2i2t B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3370, B3371, B3372, B3373 G:B2061, G:B2446 A:B2060 G:B2445, G:B2446
2otl 08014 Oph·Or G:02537(OP2) G:02102(O5') 03670, 04182, 07736, 09034 G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
2qam B3428 Oph·Or G:B2502(OP2) G:B2061(O5') B3961, B3962, B3963, B3964 G:B2061, G:B2446 C:B2501, A:B2060 A:B2060, G:B2446
2qao B3117 Oph·Or G:B2502(OP2) G:B2061(O5') B3714, B3715, B3716, B3717 G:B2061 C:B2501, A:B2060 A:B2060, G:B2446
2qb9 A2060 Oph·Or A:A1197(OP1) C:A1054(O5') A2408, A2409, A2410 G:A1198 A:A1196
2qba B3428 Oph·Or G:B2502(OP2) G:B2061(O5') B3958, B3959, B3960, B3961 G:B2061, G:B2446 A:B2060 A:B2060, G:B2446
2qbc B3117 Oph·Or G:B2502(OP2) G:B2061(O5') B3716, B3717, B3718, B3719 G:B2061, G:B2446 C:B2501, A:B2060 A:B2060, G:B2446
2qbi B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3360, B3361, B3362, B3363 G:B2061 C:B2501, A:B2060
2qbk B3006 Oph·Or U:B1379(OP2) A:B1378(O2') B3477, B3478, B3479 G:B1380 G:B1380
2qex 08093 Oph·Or G:01071(OP1) A:01070(O2') 03475, 03505, 03547, 09508 G:0627 A:0914, G:01071
2qov B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3364, B3365, B3366, B3367 G:B2061, G:B2446 A:B2060 G:B2446
2qov B3011 Oph·Or C:B510(OP1), U:B511(OP2) C:B509(O3') B3497, B3498, B3499 G:B512

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>