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

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Representative site 4qlm:A201, See in JSmolMgRNA representative site for type mer-3OP-OB     Click on the image to toggle views

Site type: mer-3Oph·Ob

Schematic drawing for

MgRNA type mer-3OP-OB
List of all 3 Mg2+ binding sites with the site type mer-3Oph·Ob 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
2qbz X201 mer-3Oph·Ob G:X100(OP2), C:X102(OP2), A:X103(OP2) U:X104(O4) X305, X306 C:X99 G:X100
4qlm A201 mer-3Oph·Ob G:A28(OP2), G:A96(OP1), C:A97(OP2) U:A98(O4) A331, A332 G:A27 G:A28
4qln A203 mer-3Oph·Ob G:A28(OP2), G:A96(OP1), C:A97(OP2) U:A98(O4) A303 G:A27 G:A28

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>