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

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Representative site 2qbb:A2114, See in JSmolMgRNA representative site for type PO-5BO         Click on the image to toggle views

Site type: Pout·5Bout

Schematic drawing for

MgRNA type PO-5BO
List of all 18 Mg2+ binding sites with the site type Pout·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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2avy A1548 Pout·5Bout A1627, A1628, A1629, A1630, A1631, A1632 G:A645 U:A593, U:A594, U:A644, G:A645, G:A646
2qbb A2114 Pout·5Bout A2461, A2462, A2463, A2464, A2465, A2466 U:A644 U:A593, G:A592, G:A646, C:A647, G:A645
3ccr 08028 Pout·5Bout 03113, 03633, 03659, 03682, 07809, 09297 G:02275 G:02271, A:02274, G:02275, U:02276, U:02115
3df1 A2199 Pout·5Bout A4200, A4201, A4202, A4203, A4204 U:A1348 G:A1370, G:A1371, U:A1351, C:A1352, U:A1372
3i1o A1540 Pout·5Bout A1616, A1617, A1618, A1619, A1620, A1621 G:A645 G:A646, U:A594, G:A645, G:A592, U:A593
3ofd A2979 Pout·5Bout A3397, A3398, A3399, A3400, A3401, A3402 G:A2454 G:A2454, C:A2496, A:A2497, G:A2455, A:A2453
3ofp A1561 Pout·5Bout A1704, A1705, A1706, A1707, A1708 A:A1349 U:A1351, G:A1371, U:A1372, A:A1350, G:A1370
3v24 A1668 Pout·5Bout A1802, A1803, A1804, A1805, A1806, A1807 G:A1057 C:A1059, G:A1058, G:A1198, U:A1199, G:A1197
4dr4 A1666 Pout·5Bout A2111, A2112, A2113, A2114, A2115 A:A583 G:A584, G:A585, C:A756, U:A757, G:A758
4dr6 A1850 Pout·5Bout A2564, A2565, A2566, A2567, A2568, A2569 G:A1057 G:A1058, G:A1053, U:A1199, C:A1059, G:A1198
4dr7 A1827 Pout·5Bout A2527, A2528, A2529, A2530, A2531, A2532 G:A1057 G:A1058, C:A1059, G:A1053, G:A1198, U:A1199
4dv7 A1866 Pout·5Bout A2250, A2251, A2252, A2253, A2254, A2255 G:A266 G:A257, G:A258, U:A256, G:A266, G:A255
4gas A1612 Pout·5Bout A1754, A1755, A1756, A1757, A1758, A1759 A:A415 G:A425, G:A416, U:A426, G:A417, U:A427
4pe9 A1604 Pout·5Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415 G:A416, U:A427, G:A417, C:A418, G:A425
4too A3066 Pout·5Bout A3495, A3496, A3497, A3498, A3499, A3500 C:A2073 G:A2242, U:A2243, U:A2074, G:A2238, A:A2241
4tov A3085 Pout·5Bout A3584, A3585, A3586, A3587, A3588, A3589 A:A933 U:A934, G:A841, U:A842, G:A843, A:A936
4tox A3072 Pout·5Bout A3522, A3523, A3524, A3525, A3526, A3527 A:A2453 A:A2453, G:A2454, A:A2497, G:A2455, C:A2496
4tp3 A3071 Pout·5Bout A3521, A3522, A3523, A3524, A3525, A3526 A:A2453 A:A2497, A:A2453, G:A2454, G:A2455, C:A2496

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>