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

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Representative site 4ji7:A1962, See in JSmolMgRNA representative site for type 2RO-2BO        Click on the image to toggle views

Site type: 2Rout·2Bout

Schematic drawing for

MgRNA type 2RO-2BO
List of all 5 Mg2+ binding sites with the site type 2Rout·2Bout 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
3v23 A3323 2Rout·2Bout A3970, A3971, A3972, A3973, A3974 G:A1707, C:A1708 G:A1707, G:A1758
4dv6 A1819 2Rout·2Bout A2225, P204, P205, P206 C:A137, G:A138 C:A137, G:A226
4ji1 A1762 2Rout·2Bout A2261, A2262, A2263, A2264, A2265, P201 G:A227, G:A138 C:A137, G:A226
4ji6 A1833 2Rout·2Bout A2623, A2624, A2625, A2626, A2627, P201 G:A227, G:A138 C:A137, G:A226
4ji7 A1962 2Rout·2Bout A3277, A3278, A3279, A3280, A3281, A3282 C:A554, C:A555 U:A30, C:A554

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>