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

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Representative site 3df2:B3302, See in JSmolMgRNA representative site for type 2PO-RO-4BO     Click on the image to toggle views

Site type: 2Pout·Rout·4Bout

Schematic drawing for

MgRNA type 2PO-RO-4BO
List of all 9 Mg2+ binding sites with the site type 2Pout·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
2qbg B2959 2Pout·Rout·4Bout B3280, B3281, B3282, B3283, B3284, B3285 A:B582, A:B1253 C:B1251 G:B583, C:B584, A:B582, G:B585
2z4l B2957 2Pout·Rout·4Bout B3258, B3259, B3260, B3261, B3262, B3263 A:B1253, G:B583 C:B1251 C:B584, G:B585, A:B582, G:B583
3df2 B3302 2Pout·Rout·4Bout B4303, B4304, B4305, B4306, B4307, B4308 A:B1253, G:B583 C:B1251 G:B583, C:B584, G:B585, A:B582
3i1r A2905 2Pout·Rout·4Bout A3046, A3047, A3048, A3049, A3050, A3051 U:A29, A:A447 A:A447 G:A473, G:A474, U:A29, C:A31
3og0 A2905 2Pout·Rout·4Bout A3042, A3043, A3044, A3045, A3046, A3047 A:A28, A:A447 A:A447 G:A474, U:A29, G:A30, C:A31
4bpn A5042 2Pout·Rout·4Bout A6103, A6104, A6105, A6106, A6107, A6108 G:A555, A:A574 A:A574 G:A555, G:A556, U:A557, U:A554
4bpo A5042 2Pout·Rout·4Bout A2106, A2107, A2108, A2109, A2110, A2114 G:A555, A:A574 A:A574 U:A554, G:A555, G:A556, U:A557
4bpp A5042 2Pout·Rout·4Bout A7683, A7684, A7685, A7686, A7687, A7688 G:A555, A:A574 A:A574 G:A555, G:A556, U:A557, U:A554
4qcv A3381 2Pout·Rout·4Bout A4323, A4324, A4325, A4326, A4327 A:A473, A:A28 A:A473 G:A500, G:A499, U:A29, G:A30

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>