`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 3df3:A2016, See in JSmolMgRNA representative site for type 2PO-3BO Click on the image to toggle views


Site type: 2Pout·3Bout

Schematic drawing for
2Pout·3Bout
MgRNA type 2PO-3BO
List of all 199 Mg2+ binding sites with the site type 2Pout·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"
Page 8 of 8 | | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4ton A1622 2Pout·3Bout A1800, A1801, A1802, A1803, A1804, A1805 G:A803, U:A804 G:A771, U:A772, G:A773
4ton A1608 2Pout·3Bout A1732, A1733, A1734, A1735, A1736, A1737 A:A315, A:A329 G:A319, A:A320, G:A318
4tov A3019 2Pout·3Bout A3287, A3288, A3289, A3290, A3291, E303 A:A616, A:A608 G:A617, G:A618, G:A619
4tov A3094 2Pout·3Bout A3628, A3629, A3630, A3631, A3632, A3633 A:A1572, G:A1422 G:A1423, G:A1424, G:A1425
4tow A1622 2Pout·3Bout A1799, A1800, A1801, A1802, A1803, A1804 G:A803, U:A804 G:A771, U:A772, G:A773
4tow A1606 2Pout·3Bout A1724, A1725, A1726, A1727, T101, T102 G:A258, G:A259 G:A258, G:A259, G:A260
4tow A1608 2Pout·3Bout A1732, A1733, A1734, A1735, A1736, A1737 A:A315, A:A329 G:A319, A:A320, G:A318
4tp1 A3094 2Pout·3Bout A3628, A3629, A3630, A3631, A3632, A3633 A:A1572, G:A1422 G:A1423, G:A1424, G:A1425
4tp1 A3019 2Pout·3Bout A3287, A3288, A3289, A3290, A3291, A3292 A:A616, A:A608 G:A618, G:A619, G:A617
4tp1 A3133 2Pout·3Bout A3787, A3788, C405, C406, C407 C:A2591, G:A2592 G:A2592, U:A2593, A:A2600
4tp2 A1606 2Pout·3Bout A1724, A1725, A1726, A1727, A1728, T101 G:A258, G:A259 G:A258, G:A260, G:A259
4tp3 A3038 2Pout·3Bout A3372, A3373, A3374, A3375, A3376, A3377 U:A1267, A:A2009 A:A2009, G:A2010, U:A2011
4tp5 A3019 2Pout·3Bout A3287, A3288, A3289, A3290, E303, E304 A:A616, A:A608 G:A617, G:A618, G:A619
4tp6 A1608 2Pout·3Bout A1732, A1733, A1734, A1735, A1736, A1737 A:A315, A:A329 G:A319, A:A320, G:A318
4tp6 A1622 2Pout·3Bout A1801, A1802, A1803, A1804, A1805, A1806 G:A803, U:A804 G:A771, U:A772, G:A773
4tpa A1606 2Pout·3Bout A1724, A1725, A1726, A1727, A1728, T101 G:A258, G:A259 G:A258, G:A260, G:A259
4tpb A3085 2Pout·3Bout A3582, A3583, A3584, A3585, A3586, A3587 G:A977, G:A976 G:A977, G:A978, A:A979
4tpb A3038 2Pout·3Bout A3372, A3373, A3374, A3375, A3376, A3377 U:A1267, A:A2009 A:A2009, G:A2010, U:A2011
4tpc A1611 2Pout·3Bout A1750, A1751, A1752, A1753, A1754, A1755 G:A803, U:A804 G:A771, U:A772, G:A773
4tpd A3093 2Pout·3Bout A3630, A3631, A3632, A3633, A3634, A3635 A:A1572, G:A1422 G:A1423, G:A1424, G:A1425
4tpd A3019 2Pout·3Bout A3288, A3289, A3290, A3291, E303, E304 A:A616, A:A608 G:A617, G:A618, G:A619
4tpe A1622 2Pout·3Bout A1802, A1803, A1804, A1805, A1806, A1807 G:A803, U:A804 G:A771, U:A772, G:A773
4tpe A1608 2Pout·3Bout A1733, A1734, A1735, A1736, A1737, A1738 A:A315, A:A329 G:A319, A:A320, G:A318
4tpf A3019 2Pout·3Bout A3285, A3286, A3287, A3288, A3289, E305 A:A616, G:A617 G:A617, G:A618, G:A619

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>