`

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

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 3df1:A2096, See in JSmolMgRNA representative site for type 4PO            Click on the image to toggle views


Site type: 4Pout

Schematic drawing for
4Pout

MgRNA type 4PO
List of all 174 Mg2+ binding sites with the site type 4Pout 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 7 of 7 | | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4too A3086 4Pout A3587, A3588, A3589, A3590, A3591 G:A561, G:A978, A:A981, C:A982
4too A3102 4Pout A3662, A3663, A3664, A3665 G:A2056, G:A2057, U:A576, A:A2503
4tou A1617 4Pout A1779, A1780, A1781, A1782, N204, N205 U:A1049, C:A1203, A:A1204, G:A1048
4tov A3012 4Pout A3249, A3250, A3251, A3252, A3253, A3254 C:A560, A:A1008, G:A2038, G:A559
4tox A3103 4Pout A3667, A3668, A3669, A3670 G:A2056, U:A576, A:A2503, G:A2057
4tp0 N201 4Pout A1781, A1782, A1783, A1784, N302, N303 U:A1049, C:A1203, A:A1204, G:A1048
4tp1 A3012 4Pout A3250, A3251, A3252, A3253, A3254, A3255 C:A560, A:A1008, G:A2038, G:A559
4tp3 A3056 4Pout A3450, A3451, A3452, A3453, C302 A:A1772, G:A1973, G:A1828, G:A1972
4tp4 N201 4Pout A1779, A1780, A1781, N304, N305, N306 A:A1204, G:A1048, U:A1049, C:A1203
4tp7 A3103 4Pout A3664, A3665, A3666, A3667 G:A2056, U:A576, A:A2503, G:A2057
4tp7 A3043 4Pout A3381, A3382, A3383, A3384, T101 U:A1313, G:A1333, G:A1334, C:A1335
4tp7 A3059 4Pout A3458, A3459, A3460, A3461 G:A1968, G:A2592, G:A1972, G:A1973
4tp7 A3012 4Pout A3249, A3250, A3251, A3252, A3253, J201 G:A559, A:A1008, G:A2038, C:A560
4tp7 A3026 4Pout A3309, A3310, A3311, C303, C304 G:A784, A:A2589, G:A2588, G:A2599
4tp7 A3087 4Pout A3588, A3589, A3590, A3591, A3592 A:A981, G:A977, G:A978, C:A982
4tp9 A3012 4Pout A3250, A3251, A3252, A3253, A3254, J201 C:A560, A:A1008, G:A2038, G:A559
4tpb A3040 4Pout A3382, A3383, A3384, A3385 A:A2005, C:A2006, A:A1268, A:A1269
4tpc A1617 4Pout A1779, A1780, A1781, A1782, N204, N205 C:A1203, A:A1204, G:A1048, U:A1049
4tpd A3012 4Pout A3250, A3251, A3252, A3253, A3254, A3255 C:A560, A:A1008, G:A2038, G:A559
4tpf A3043 4Pout A3384, A3385, A3386, A3387, T101 U:A1313, G:A1333, G:A1334, C:A1335
4tpf A3012 4Pout A3249, A3250, A3251, A3252, A3253, J201 G:A559, A:A1008, G:A2038, C:A560
4tpf A3059 4Pout A3461, A3462, A3463, A3464 G:A1968, G:A2592, G:A1972, G:A1973
4tra A79 4Pout A193, A194, A195, A196, A197, A198 U:A12, U:A8, A:A9, C:A11
6tna A79 4Pout A154, A155, A156, A157, A158, A159 U:A12, U:A8, A:A9, C:A11

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>