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

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Representative site 2qbk:B2987, See in JSmolMgRNA representative site for type 5PO-2BO        Click on the image to toggle views

Site type: 5Pout·2Bout

Schematic drawing for

MgRNA type 5PO-2BO
List of all 10 Mg2+ binding sites with the site type 5Pout·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
2qao B3485 5Pout·2Bout B4014, B4015, B4016, B4017, B4018, B4019 U:B2613, C:B2050, A:B2051, G:B2578, A:B2614 A:B2051, A:B2614
2qbk B2987 5Pout·2Bout B3409, B3410, B3411, B3412, B3413, B3414 U:B2613, C:B2050, A:B2614, A:B2051, G:B2578 A:B2051, A:B2614
3v23 A3607 5Pout·2Bout A5036, A5037, A5038, A5039, A5040, A5041 U:A2613, G:A2578, C:A2050, A:A2051, A:A2614 A:A2051, A:A2614
3v25 A3417 5Pout·2Bout A4136, A4137, A4138, A4139, A4140, A4141 G:A2578, A:A2614, A:A2051, U:A2613, C:A2050 A:A2614, A:A2051
3v27 A3563 5Pout·2Bout A4933, A4934, A4935, A4936, A4937 A:A213, G:A177, G:A179, G:A178, G:A212 G:A178, G:A179
3v29 A3573 5Pout·2Bout A4667, A4668, A4669, A4670, A4671, A4672 G:A2578, A:A2614, A:A2051, U:A2613, C:A2050 A:A2051, A:A2614
4nxn A1632 5Pout·2Bout A1966, A1967, A1968, A1969 A:A563, G:A557, G:A558, U:A560, C:A562 A:A300, G:A566
4qcp A3575 5Pout·2Bout A4824, A4825, A4826, A4827, A4828, A4829 A:A2051, G:A2578, A:A2614, U:A2613, C:A2050 A:A2051, A:A2614
4qct A3591 5Pout·2Bout A4846, A4847, A4848, A4849, A4850, A4851 A:A2051, A:A2614, U:A2613, C:A2050, G:A2578 A:A2051, A:A2614
4qd1 A3581 5Pout·2Bout A4674, A4675, A4676, A4677, A4678, A4679 A:A2051, G:A2578, A:A2614, U:A2613, C:A2050 A:A2051, A:A2614

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>