MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbb:A2114, See in JSmolClick on the image to toggle views Site type: Pout·5Bout Schematic drawing for Pout·5Bout 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" 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 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
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].

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