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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
2qox B2924 Oph·Or G:B2502(OP2) G:B2061(O5') B3110, B3111, B3112, B3113 G:B2061, G:B2446 A:B2060, G:B2502
2qp1 B3006 Oph·Or U:B1379(OP2) A:B1378(O2') B3987, B3988, B3989 G:B1380 G:B1380
2z4l B3007 Oph·Or G:B1380(OP2) A:B1378(O2') B3477, B3478, B3479 U:B1379
2z4l B2979 Oph·Or G:B2502(OP2) G:B2061(O5') B3362, B3363, B3364, B3365 G:B2061, G:B2446 A:B2060, G:B2502 G:B2446
2z4n B2925 Oph·Or G:B2502(OP2) G:B2061(O5') B3112, B3113, B3114, B3115 G:B2061, G:B2446 A:B2060, G:B2502 G:B2446
3cc7 08010 Oph·Or G:02537(OP2) G:02102(O5') 03693, 04211, 07805, 09040 G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
3df2 B3428 Oph·Or G:B2502(OP2) G:B2061(O5') B4429, B4430, B4431, B4432 G:B2061, G:B2446 A:B2060 G:B2446
3df4 B3117 Oph·Or G:B2502(OP2) G:B2061(O5') B4118, B4119, B4120, B4121 G:B2061, G:B2446 A:B2060 G:B2446
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
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
3owz B116 Oph·Or A:B33(OP2) G:B32(O2') B151, B152, B153, B154 C:B66 U:B67, U:B69
3owz A102 Oph·Or A:A33(OP2) G:A32(O2') A123, A124, A125, A126 C:A66 C:A68, U:A69, U:A67
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
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
4en5 A109 Oph·Or A:A40(OP2) A210, A211, A212, A213 A:A49, C:A50
4gas A1641 Oph·Or G:A1505(OP1) A:A1507(O3') A1887, A1888, A1889 C:A1501, G:A1504 U:A1506
4gau A3071 Oph·Or C:A2611(OP2) G:A2576(O2') A3540, A3541, A3542, A3543 C:A2579, U:A2580 C:A2610 G:A2505, G:A2581
4kix A3126 Oph·Or C:A510(OP1), U:A511(OP2) C:A509(O3') A3758, A3759, A3760 G:A512
4nvv A3590 Oph·Or G:A991(OP2) A:A990(O5') A4811, A4812, A4813, A4814 U:A869, A:A990 G:A989
4tp3 A3114 Oph·Or C:A2573(OP1) A:A2572(O2') A3707, A3708, A3709 G:A2574, C:A2575, C:A2507
4tp3 A3064 Oph·Or G:A2502(OP2) G:A2061(O5') A3488, A3489, A3490, A3491 A:A2062 A:A2060 G:A2446, G:A2445

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>