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

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 4tpc:A1604, See in JSmolMgRNA representative site for type 2PO-5BO        Click on the image to toggle views

Site type: 2Pout·5Bout

Schematic drawing for

MgRNA type 2PO-5BO
List of all 12 Mg2+ binding sites with the site type 2Pout·5Bout 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 1 of 1
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3v23 A3316 2Pout·5Bout A3941, A3942, A3943, A3944, A3945, A3946 C:A66, U:A67 G:A58, G:A68, C:A69, U:A59, U:A67
3v29 A3386 2Pout·5Bout A3961, A3962, A3963, A3964, A3965, A3966 G:A686, C:A687 G:A690, U:A688, A:A689, G:A771, C:A772
3v2f A3314 2Pout·5Bout A4302, A4303, A4304, A4305 A:A1214, A:A1213 G:A1215, G:A1216, U:A1234, A:A1214, G:A1235
4ji6 A1834 2Pout·5Bout A2628, A2629, A2630, A2631, A2632, A2633 A:A414, A:A415 G:A426, U:A427, G:A428, A:A415, G:A416
4ji7 A1886 2Pout·5Bout A2832, A2833, A2834, A2835, A2836, A2837 A:A414, A:A415 G:A416, G:A426, U:A427, G:A428, A:A415
4ji8 A1866 2Pout·5Bout A2718, A2719, A2720, A2721, A2722, A2723 A:A414, A:A415 G:A426, U:A427, G:A428, G:A416, C:A417
4peb A3131 2Pout·5Bout A3788, A3789, A3790, A3791, A3792, C305 A:A1791, C:A1790 G:A1792, G:A1828, C:A1793, G:A1826, U:A1827
4too A3071 2Pout·5Bout A3519, A3520, A3521, A3522, A3523, A3524 A:A2453, C:A2452 A:A2453, G:A2454, A:A2497, G:A2455, C:A2496
4tp4 A1604 2Pout·5Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415, G:A416 G:A416, U:A426, G:A417, C:A418, G:A425
4tp5 A3132 2Pout·5Bout A3787, A3788, A3789, A3790, A3791, A3792 A:A1791, C:A1790 G:A1828, C:A1793, G:A1792, G:A1826, U:A1827
4tpc A1604 2Pout·5Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415, G:A416 G:A416, G:A417, U:A426, C:A418, G:A425
4tpd A3132 2Pout·5Bout A3790, A3791, A3792, A3793, A3794, A3795 C:A1790, A:A1791 G:A1828, C:A1793, G:A1792, G:A1826, U:A1827

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>