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

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Representative site 1vs8:B2932, See in JSmolMgRNA representative site for type 3PO            Click on the image to toggle views


Site type: 3Pout

Schematic drawing for
3Pout

MgRNA type 3PO
List of all 207 Mg2+ binding sites with the site type 3Pout 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
4tpb A3039 3Pout A3378, A3379, A3380, A3381 A:A1268, C:A2006, G:A2048
4tpb A3102 3Pout A3665, A3666, A3667, A3668 G:A2056, G:A2057, U:A576
4tpb A3056 3Pout A3450, A3451, A3452, A3453, C302 A:A1772, G:A1828, G:A1972
4tpb A3058 3Pout A3460, A3461, A3462, A3463 G:A1972, G:A1973, G:A2592
4tpe A1631 3Pout A1846, A1847, A1848, A1849, A1850, N203 G:A1048, U:A1049, A:A1204
4tpf A3137 3Pout A3800, A3801, A3802, A3803, A3804, N202 C:A2874, G:A2838, G:A2819
4tpf A3087 3Pout A3591, A3592, A3593, A3594, A3595 A:A981, G:A978, C:A982

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>