`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
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"
Page 5 of 6 | | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4pea A1620 Pout·4Bout A1788, A1789, A1790, A1791, A1792, A1793 G:A645 G:A645, G:A646, G:A592, U:A593
4pea A1605 Pout·4Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259, C:A267
4peb A3070 Pout·4Bout A3527, A3528, A3529, A3530, A3531, A3532 A:A2453 A:A2453, G:A2454, A:A2497, G:A2455
4pec A3102 Pout·4Bout A3669, A3670, A3671, A3672, A3673, A3674 C:A2616 G:A2049, C:A2047, G:A2048, G:A2618
4qcn A3653 Pout·4Bout A5082, A5083, A5084, A5085, A5086, A5087 A:A1748 G:A1749, G:A1746, G:A1750, G:A1794
4qct A3383 Pout·4Bout A4364, A4365, A4366, A4367, A4368 G:A2845 G:A2848, U:A2847, G:A2845, G:A2846
4qcx A3379 Pout·4Bout A4287, A4288, A4289, A4290, A4291 A:A2453 A:A2453, A:A2497, G:A2454, G:A2455
4qcx A3384 Pout·4Bout A4300, A4301, A4302, A4303, A4304 G:A2845 G:A2848, G:A2846, U:A2847, G:A2845
4qcz A3513 Pout·4Bout A4662, A4663, A4664, A4665, A4666, A4667 A:A101 G:A79, G:A80, G:A78, G:A81
4qcz A3651 Pout·4Bout A4986, A4987, A4988, A4989, A4990, A4991 A:A1748 G:A1794, G:A1746, G:A1749, G:A1750
4tom A3083 Pout·4Bout A3582, A3583, A3584, A3585, A3586, A3587 A:A933 G:A841, U:A842, G:A843, A:A936
4ton A1612 Pout·4Bout A1751, A1752, A1753, A1754, A1755, A1756 A:A415 G:A417, G:A425, U:A426, G:A416
4too A3094 Pout·4Bout A3625, A3626, A3627, A3628 A:A1439 A:A1552, U:A1440, G:A1441, A:A1551
4tou A1604 Pout·4Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415 G:A416, G:A417, C:A418, G:A425
4tou A1610 Pout·4Bout A1744, A1745, A1746, A1747, A1748, A1749 U:A644 G:A646, U:A593, U:A594, G:A645
4tow A1630 Pout·4Bout A1839, A1840, A1841, A1842, N201, N202 A:A1360 A:A1360, G:A1361, C:A979, C:A980
4tow A1612 Pout·4Bout A1750, A1751, A1752, A1753, A1754, A1755 A:A415 G:A417, G:A425, U:A426, G:A416
4tox A3019 Pout·4Bout A3286, A3287, A3288, A3289, A3290, A3291 A:A616 G:A617, G:A619, G:A618, C:A610
4tp0 A1610 Pout·4Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A645 G:A646, U:A593, U:A594, G:A645
4tp2 A1605 Pout·4Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259, C:A267
4tp3 A3103 Pout·4Bout A3669, A3670, A3671, A3672, A3673, A3674 C:A2616 G:A2049, G:A2618, C:A2047, G:A2048
4tp4 A1622 Pout·4Bout A1804, A1805, A1806, A1807, A1808, A1809 G:A266 G:A257, G:A259, G:A258, U:A268
4tp5 A3071 Pout·4Bout A3525, A3526, A3527, A3528, A3529, A3530 C:A2452 A:A2453, G:A2454, A:A2497, G:A2455
4tp6 A1605 Pout·4Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259, C:A267
4tp6 A1612 Pout·4Bout A1752, A1753, A1754, A1755, A1756, A1757 A:A415 G:A417, U:A426, G:A425, G:A416

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>