`

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

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 2qbe:B3457, See in JSmolMgRNA representative site for type 2PO-4BO        Click on the image to toggle views


Site type: 2Pout·4Bout

Schematic drawing for
2Pout·4Bout

MgRNA type 2PO-4BO
List of all 68 Mg2+ binding sites with the site type 2Pout·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"
Page 3 of 3 | | Next » | 1 | 2 | 3
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4ji1 A1756 2Pout·4Bout A2225, A2226, A2227, A2228, A2229, A2230 A:A431, G:A407 G:A409, G:A410, A:A408, G:A407
4pea A1612 2Pout·4Bout A1750, A1751, A1752, A1753, A1754, A1755 G:A416, A:A415 G:A417, G:A425, U:A426, G:A416
4qcn A3466 2Pout·4Bout A4569, A4570, A4571, A4572, A4573 G:A2855, G:A2856 U:A2857, G:A2858, G:A2855, G:A2856
4qcp A3374 2Pout·4Bout A4345, A4346, A4347, A4348, A4349, A4350 C:A2452, A:A2453 A:A2453, G:A2455, A:A2497, G:A2454
4qcp A3379 2Pout·4Bout A4357, A4358, A4359, A4360, A4361 G:A2845, G:A2846 U:A2847, G:A2848, G:A2845, G:A2846
4qct A3379 2Pout·4Bout A4354, A4355, A4356, A4357, A4358, A4359 C:A2452, A:A2453 A:A2453, A:A2497, G:A2454, G:A2455
4qcv A3444 2Pout·4Bout A4471, A4472, A4473, A4474, A4475, A4476 C:A2464, A:A2465 A:A2465, A:A2509, G:A2466, G:A2467
4qcz A3471 2Pout·4Bout A4534, A4535, A4536, A4537, A4538 G:A2855, G:A2856 U:A2857, G:A2858, G:A2855, G:A2856
4qd1 A3390 2Pout·4Bout A4277, A4278, A4279, A4280, A4281, A4282 C:A2452, A:A2453 A:A2453, A:A2497, G:A2454, G:A2455
4tol A1604 2Pout·4Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415, G:A416 G:A416, G:A417, G:A425, U:A426
4tov A3072 2Pout·4Bout A3524, A3525, A3526, A3527, A3528, A3529 A:A2453, C:A2452 A:A2453, A:A2497, G:A2454, G:A2455
4tp0 A1604 2Pout·4Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415, G:A416 G:A417, C:A418, U:A426, G:A416
4tp2 A1612 2Pout·4Bout A1752, A1753, A1754, A1755, A1756, A1757 G:A416, A:A415 G:A417, G:A425, U:A426, G:A416
4tp2 A1622 2Pout·4Bout A1801, A1802, A1803, A1804, A1805, A1806 G:A803, U:A804 G:A771, U:A772, A:A807, G:A773
4tp3 A3019 2Pout·4Bout A3287, A3288, A3289, A3290, A3291, E304 A:A616, A:A608 G:A617, G:A618, C:A610, G:A619
4tp7 A3072 2Pout·4Bout A3519, A3520, A3521, A3522, A3523, A3524 A:A2453, C:A2452 A:A2497, A:A2453, G:A2454, G:A2455
4tp8 A1604 2Pout·4Bout A1715, A1716, A1717, A1718, A1719, A1720 G:A416, A:A415 G:A416, G:A417, U:A426, G:A425
4tpa A1622 2Pout·4Bout A1801, A1802, A1803, A1804, A1805, A1806 G:A803, U:A804 G:A771, U:A772, A:A807, G:A773

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>