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

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Representative site 3df2:B3509, See in JSmolMgRNA representative site for type fac-3OP-OR     Click on the image to toggle views

Site type: fac-3Oph·Or

Schematic drawing for

MgRNA type fac-3OP-OR
List of all 3 Mg2+ binding sites with the site type fac-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
2qov B2994 fac-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3429, B3430
2qoz B2994 fac-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3919, B3920 C:B1135
3df2 B3509 fac-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B4510, B4511

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>