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

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Representative site 2qao:B3525, See in JSmolMgRNA representative site for type mer-3OP-OR     Click on the image to toggle views


Site type: mer-3Oph·Or

Schematic drawing for
mer-3Oph·Or

MgRNA type mer-3OP-OR
List of all 19 Mg2+ binding sites with the site type mer-3Oph·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
1vs6 B2994 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3429, B3430 C:B1135
1vs8 B2994 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3436, B3437 C:B1135
2aw4 B2994 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3425, B3426 C:B1135
2awb B2995 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3437, B3438 C:B1135
2i2v B2995 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3445, B3446 C:B1135
2qam B3509 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B4026, B4027 C:B1135
2qao B3525 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B4045, B4046 C:B1135
2qba B3509 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B4023, B4024 C:B1135
2qbc B3525 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B4045, B4046 C:B1135
2qbe B3509 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B4023, B4024 C:B1135
2qbg B2996 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3444, B3445 C:B1135
2qbi B2994 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3425, B3426 C:B1135
2qbk B2996 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3440, B3441 C:B1135
2qox B2995 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3440, B3441
2qp1 B2996 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3948, B3949
2z4l B2995 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3427, B3428 C:B1135
2z4n B2997 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3442, B3443 C:B1135
3df4 B3525 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B4526, B4527 C:B1135
3i9b A1966 mer-3Oph·Or C:A1054(OP1), G:A1197(OP1), G:A1198(OP2)

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>