MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·2Bout Schematic drawing for 2Pout·2Bout List of all 279 Mg2+ binding sites with the site type 2Pout·2Bout 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 12 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3oaq A1 2Pout·2Bout A1577, A1578, A1579, A1580, A1581, A1582 G:A259, G:A258 G:A259, G:A260 3ofx A1 2Pout·2Bout A1576, A1577, A1578, A1579, A1580, A1581 G:A259, G:A258 G:A259, G:A260 3i21 A1 2Pout·2Bout A1573, A1574, A1575, A1576, T87, T88 G:A258, G:A259 G:A260, G:A259 3i1s A1 2Pout·2Bout A1573, A1574, A1575, A1576, T87, T88 G:A258, G:A259 G:A260, G:A259 3ofa A1 2Pout·2Bout A1576, A1577, A1578, A1579, A1580, A1581 G:A259, G:A258 G:A260, G:A259 3or9 A1 2Pout·2Bout A1577, A1578, A1579, A1580, A1581, A1582 G:A259, G:A258 G:A260, G:A259 3ora A1 2Pout·2Bout A1576, A1577, A1578, A1579, A1580, A1581 G:A258, G:A259 G:A260, G:A259 3i1o A4 2Pout·2Bout A1588, A1589, A1590, A1591, A1592, A1593 A:A415, G:A416 G:A417, G:A416 4a1e 05 2Pout·2Bout 05043, 05044, 05045, 05046, 05047, 05048 G:2137, U:2136 G:2137, U:2138 4a17 05 2Pout·2Bout 05043, 05044, 05045, 05046, 05047, 05048 G:2137, U:2136 G:2137, U:2138 4m4o B103 2Pout·2Bout B245, B246, B247, B248, B277 C:B39, U:B38 A:B25, G:B26 3ox0 B124 2Pout·2Bout B149, B150, B151, B152, B153 C:B24, U:B23 G:B25, G:B26 3oxd B131 2Pout·2Bout B149, B150, B151, B152, B153, B154 U:B23, G:B25 G:B25, G:B26 3oxd B133 2Pout·2Bout B161, B162, B163, B164, B165, B166 C:B35, A:B34 G:B36, A:B37 3dil A229 2Pout·2Bout A1240, A1241, A1242, A1243, A1244 A:A23, A:A66 U:A24, G:A25 1yls B242 2Pout·2Bout B355, B356, B357, B358, B359, B360 C:B215, G:B216 G:B216, G:B217 4gau E301 2Pout·2Bout A3286, A3287, A3288, E403, E404, E405 A:A616, A:A608 G:A617, G:A618 3p49 A738 2Pout·2Bout A755, A756, A757, A758 G:A151, G:A152 G:A85, U:A83 3ofp A1535 2Pout·2Bout A1578, A1579, A1580, A1581, A1582, A1583 A:A315, A:A329 G:A319, G:A318 3i1z A1535 2Pout·2Bout A1583, A1584, A1585, A1586, A1587, A1588 A:A329, A:A315 G:A318, G:A319 3oaq A1537 2Pout·2Bout A1593, A1594, A1595, A1596, A1597, A1598 A:A415, G:A416 G:A417, G:A416 3i1q A1537 2Pout·2Bout A1590, A1591, A1592, A1593, A1594, A1595 A:A415, G:A416 G:A417, G:A425 3i21 A1541 2Pout·2Bout A1622, A1623, A1624, A1625, A1626, A1627 G:A803, U:A804 G:A771, G:A773 3i1s A1541 2Pout·2Bout A1622, A1623, A1624, A1625, A1626, A1627 G:A803, U:A804 G:A771, G:A773 3i1o A1541 2Pout·2Bout A1622, A1623, A1624, A1625, A1626, A1627 G:A803, U:A804 G:A771, 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].

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