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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
3owz A102 Oph·Or A:A33(OP2) G:A32(O2') A123, A124, A125, A126 C:A66 C:A68, U:A69, U:A67
4en5 A109 Oph·Or A:A40(OP2) A210, A211, A212, A213 A:A49, C:A50
3owz B116 Oph·Or A:B33(OP2) G:B32(O2') B151, B152, B153, B154 C:B66 U:B67, U:B69
3ofp A1538 Oph·Or A:A510(OP2) A:A509(O5') A1595, A1596, A1597, A1598 A:A509, G:A506, C:A507 U:A508 A:A510
3ofy A1538 Oph·Or A:A510(OP2) A:A509(O5') A1595, A1596, A1597, A1598 A:A509, G:A506, C:A507 U:A508 A:A510
2i2p A1585 Oph·Or G:A1068(OP1) G:A1387(O2') A1810, A1811, A1812, A1813 G:A1094
1vvz A1640 Oph·Or U:A1376(OP2) ARG:G94(NH1)
4gas A1641 Oph·Or G:A1505(OP1) A:A1507(O3') A1887, A1888, A1889 C:A1501, G:A1504 U:A1506
3v26 A1698 Oph·Or A:A509(OP2) A1891, A1892, A1893, A1894 G:A506, C:A507 A:A510
4dr4 A1749 Oph·Or G:A1197(OP1) C:A1054(O5') A2292, A2293, A2294 G:A1198 U:A1196
2qb9 A2060 Oph·Or A:A1197(OP1) C:A1054(O5') A2408, A2409, A2410 G:A1198 A:A1196
2qox B2924 Oph·Or G:B2502(OP2) G:B2061(O5') B3110, B3111, B3112, B3113 G:B2061, G:B2446 A:B2060, G:B2502
2z4n B2925 Oph·Or G:B2502(OP2) G:B2061(O5') B3112, B3113, B3114, B3115 G:B2061, G:B2446 A:B2060, G:B2502 G:B2446
3r8s A2967 Oph·Or G:A2502(OP2) G:A2061(O5') A3392, A3393, A3394, A3395 G:A2061 C:A2501, A:A2060 A:A2060, G:A2445, G:A2446
3i1n A2967 Oph·Or G:A2502(OP2) A:A2060(O2') A3338, A3339, A3340, A3341 G:A2061 A:A2060, G:A2445, G:A2446
3i20 A2967 Oph·Or G:A2502(OP2) A:A2060(O2') A3336, A3337, A3338, A3339 G:A2061 A:A2060, G:A2446
2i2t B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3370, B3371, B3372, B3373 G:B2061, G:B2446 A:B2060 G:B2445, G:B2446
2aw4 B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3360, B3361, B3362, B3363 G:B2061 A:B2060 A:B2060, G:B2446
2qov B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3364, B3365, B3366, B3367 G:B2061, G:B2446 A:B2060 G:B2446
2qbi B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3360, B3361, B3362, B3363 G:B2061 C:B2501, A:B2060
1vs6 B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3364, B3365, B3366, B3367 G:B2061 A:B2060 A:B2060, G:B2446
2z4l B2979 Oph·Or G:B2502(OP2) G:B2061(O5') B3362, B3363, B3364, B3365 G:B2061, G:B2446 A:B2060, G:B2502 G:B2446
2awb B3005 Oph·Or U:B1379(OP2) A:B1378(O2') B3475, B3476, B3477 G:B1380 G:B1380
2qp1 B3006 Oph·Or U:B1379(OP2) A:B1378(O2') B3987, B3988, B3989 G:B1380 G:B1380
2qbk B3006 Oph·Or U:B1379(OP2) A:B1378(O2') B3477, B3478, B3479 G:B1380 G:B1380

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>