MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoz:B2982, See in JSmolClick on the image to toggle views Site type: Pout·3Bout Schematic drawing for Pout·3Bout List of all 341 Mg2+ binding sites with the site type Pout·3Bout 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 6 of 14 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3ofa A1556 Pout·3Bout A1687, A1688, A1689, A1690, A1691, A1692 A:A781 G:A800, U:A798, G:A799 3ofa A1555 Pout·3Bout A1681, A1682, A1683, A1684, A1685, A1686 G:A266 G:A257, G:A259, G:A258 3ofb A1556 Pout·3Bout A1680, A1681, A1682, A1683, A1684, A1685 A:A781 G:A799, G:A800, U:A798 3ofb A1555 Pout·3Bout A1674, A1675, A1676, A1677, A1678, A1679 G:A266 G:A257, G:A259, G:A258 3ofc A2985 Pout·3Bout A3422, A3423, A3424, A3425, A3426, A3427 A:A933 G:A841, U:A842, A:A936 3ofd A2925 Pout·3Bout A3145, A3146, A3147, A3148, A3149, A3150 U:A755 G:A757, A:A739, A:A756 3ofo A1554 Pout·3Bout A1678, A1679, A1680, A1681, A1682, A1683 G:A266 G:A257, G:A259, G:A258 3ofo A1555 Pout·3Bout A1684, A1685, A1686, A1687, A1688, A1689 A:A781 G:A799, G:A800, U:A798 3ofp A1556 Pout·3Bout A1678, A1679, A1680, A1681, A1682, A1683 A:A781 G:A800, U:A798, G:A799 3ofp A1555 Pout·3Bout A1672, A1673, A1674, A1675, A1676, A1677 G:A266 G:A257, G:A259, G:A260 3ofp A1543 Pout·3Bout A1617, A1618, A1619, A1620, A1621, A1622 G:A645 G:A592, G:A646, G:A645 3ofq A2980 Pout·3Bout A3399, A3400, A3401, A3402, A3403, A3404 A:A2453 G:A2454, A:A2497, G:A2455 3ofq A2943 Pout·3Bout A3225, A3226, A3227, A3228, A3229, A3230 U:A1267 A:A2009, G:A2010, U:A2011 3ofq A2977 Pout·3Bout A3383, A3384, A3385, A3386, A3387 C:A2310 G:A2304, U:A2302, G:A2303 3ofx A1556 Pout·3Bout A1687, A1688, A1689, A1690, A1691, A1692 A:A781 G:A800, U:A798, G:A799 3ofx A1555 Pout·3Bout A1681, A1682, A1683, A1684, A1685, A1686 G:A266 G:A257, G:A259, G:A258 3ofy A1556 Pout·3Bout A1681, A1682, A1683, A1684, A1685, A1686 A:A781 G:A799, G:A800, U:A798 3ofy A1561 Pout·3Bout A1707, A1708, A1709, A1710, I169 U:A1348 G:A1371, U:A1372, G:A1370 3ofz A3034 Pout·3Bout A3621, A3622, A3623, A3624, A3625, 4764 A:A2741 G:A2742, G:A2763, U:A2743 3ofz A2984 Pout·3Bout A3411, A3412, A3413, A3414, A3415, A3416 A:A933 U:A842, G:A843, A:A936 3or9 A1557 Pout·3Bout A1688, A1689, A1690, A1691, A1692, A1693 A:A781 G:A800, U:A798, G:A799 3or9 A1544 Pout·3Bout A1627, A1628, A1629, A1630, A1631, A1632 G:A803 G:A771, U:A772, G:A773 3or9 A1556 Pout·3Bout A1682, A1683, A1684, A1685, A1686, A1687 G:A266 G:A257, G:A259, G:A258 3or9 A1549 Pout·3Bout A1653, A1654, N101, N102, N103, N104 A:A1360 G:A1361, C:A980, A:A1360 3ora A1556 Pout·3Bout A1685, A1686, A1687, A1688, A1689, A1690 A:A781 G:A799, G:A800, U:A798

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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