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

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Representative site 3i1r:A2920, See in JSmolMgRNA representative site for type PO-2RO-3BO     Click on the image to toggle views


Site type: Pout·2Rout·3Bout

Schematic drawing for
Pout·2Rout·3Bout

MgRNA type PO-2RO-3BO
List of all 5 Mg2+ binding sites with the site type Pout·2Rout·3Bout 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
4ji3 A1663 Pout·2Rout·3Bout A2015, A2016, A2017, A2018 C:A352 G:A331, C:A352 C:A330, A:A59, G:A354
4ji1 A1784 Pout·2Rout·3Bout A2393, A2394, A2395, A2396, A2397, A2398 G:A21 G:A567, G:A568 G:A567, A:A563, A:A573
3i1r A2920 Pout·2Rout·3Bout A3123, A3124, A3125, A3126, A3127, Q226 A:A1253 C:A1251, A:A582 G:A583, C:A584, G:A585
3oat A2996 Pout·2Rout·3Bout A3469, A3470, A3471, A3472, A3473, A3474 C:A1617 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
4dha A3729 Pout·2Rout·3Bout A4823, A4824, A4825, A4826, A4827, A4828 U:A1211 G:A307, A:A1210 G:A308, G:A309, G:A1212

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>