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

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Representative site 3df2:B3103, See in JSmolMgRNA representative site for type PO-RO-4BO      Click on the image to toggle views

Site type: Pout·Rout·4Bout

Schematic drawing for

MgRNA type PO-RO-4BO
List of all 6 Mg2+ binding sites with the site type Pout·Rout·4Bout 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
3df2 B3103 Pout·Rout·4Bout B4104, B4105, B4106, B4107, B4108, B4109 U:B1267 G:B1266 G:B2010, U:B2011, G:B2012, A:B2009
3i1n A2941 Pout·Rout·4Bout A3217, A3218, A3219, A3220, A3221, A3222 U:A1267 G:A1266 G:A2010, U:A2011, G:A2012, A:A2009
4bpe A5042 Pout·Rout·4Bout A2108, A2109, A2110, A2111, A2112, A2117 A:A574 A:A574 U:A554, G:A555, G:A556, U:A557
4gar A3036 Pout·Rout·4Bout A3375, A3376, A3377, A3378, A3379, A3380 U:A1267 G:A1266 G:A2010, G:A2012, A:A1269, U:A2011
4qcr A3680 Pout·Rout·4Bout A5111, A5112, A5113, A5114, A5115, A5116 A:A1748 G:A1746 G:A1746, G:A1749, G:A1750, G:A1794
4too A3061 Pout·Rout·4Bout A3472, A3473, A3474, A3475 A:A2033 A:A2033 U:A2026, G:A2027, U:A2028, G:A2029

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>