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

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Representative site 2qbg:B2930, See in JSmolMgRNA representative site for type PO-4BO         Click on the image to toggle views


Site type: Pout·4Bout

Schematic drawing for
Pout·4Bout

MgRNA type PO-4BO
List of all 135 Mg2+ binding sites with the site type Pout·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
4tp7 A3085 Pout·4Bout A3576, A3577, A3578, A3579, A3580, A3581 A:A933 U:A842, G:A843, U:A934, G:A841
4tp7 A3094 Pout·4Bout A3620, A3621, A3622, A3623, A3624, A3625 A:A1572 G:A1423, G:A1424, C:A1574, G:A1425
4tp9 A3085 Pout·4Bout A3583, A3584, A3585, A3586, A3587, A3588 A:A933 G:A843, G:A841, U:A842, A:A936
4tpb A3131 Pout·4Bout A3780, A3781, A3782, A3783, A3784, C307 C:A1790 C:A1793, U:A1825, G:A1826, U:A1827
4tpb A3071 Pout·4Bout A3521, A3522, A3523, A3524, A3525, A3526 A:A2453 A:A2497, A:A2453, G:A2454, G:A2455
4tpb A3019 Pout·4Bout A3287, A3288, A3289, A3290, A3291, A3292 A:A608 G:A617, G:A618, C:A610, G:A619
4tpc A1623 Pout·4Bout A1805, A1806, A1807, A1808, A1809, A1810 G:A266 G:A257, G:A259, G:A258, U:A268
4tpe A1612 Pout·4Bout A1753, A1754, A1755, A1756, A1757, A1758 A:A415 G:A416, G:A417, G:A425, U:A426
4tpf A3094 Pout·4Bout A3623, A3624, A3625, A3626, A3627, A3628 A:A1572 G:A1423, G:A1424, C:A1574, G:A1425
4tpf A3096 Pout·4Bout A3633, A3634, A3635, A3636, A3637, A3638 G:A1444 G:A1464, G:A1445, C:A1446, G:A1465

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>