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 JSmolClick on the image to toggle views Site type: Pout·4Bout Schematic drawing for Pout·4Bout 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 1 of 6 | « Previous | Next » | 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 1hr2 B17 Pout·4Bout B362, B363, B364, B365, B366, B367 A:B114 A:B115, G:B116, U:B205, G:B117 3ivk C132 Pout·4Bout C177, C178, C179, C180, C181, C182 A:C-4 A:C-4, A:C14, G:C-3, U:C-2 4a1c 0204 Pout·4Bout 06291, 06292, 06293, 06294, 06295, 06296 A:374 U:376, A:3101, G:3102, A:3100 4a1a 0204 Pout·4Bout 06675, 06676, 06677, 06678, 06679, 06680 A:374 U:376, A:3101, G:3102, A:3100 3ofp A1537 Pout·4Bout A1589, A1590, A1591, A1592, A1593, A1594 A:A415 G:A417, G:A425, G:A416, U:A426 3ofa A1537 Pout·4Bout A1592, A1593, A1594, A1595, A1596, A1597 A:A415 G:A417, C:A418, G:A416, U:A426 3ofo A1537 Pout·4Bout A1591, A1592, A1593, A1594, A1595, A1596 A:A415 G:A417, C:A418, G:A416, U:A426 3i21 A1540 Pout·4Bout A1616, A1617, A1618, A1619, A1620, A1621 G:A645 C:A647, G:A645, G:A592, U:A593 3oar A1543 Pout·4Bout A1616, A1617, A1618, A1619, A1620, A1621 G:A645 G:A646, G:A645, G:A592, U:A593 3ofb A1543 Pout·4Bout A1617, A1618, A1619, A1620, A1621, A1622 G:A645 G:A646, G:A645, G:A592, U:A593 3i1q A1543 Pout·4Bout A1618, A1619, A1620, A1621, A1622, A1623 G:A645 G:A646, G:A592, U:A593, G:A645 3ofy A1543 Pout·4Bout A1617, A1618, A1619, A1620, A1621, A1622 G:A645 G:A646, G:A645, G:A592, U:A593 2qoy A1548 Pout·4Bout A1924, A1925, A1926, A1927, A1928, A1929 U:A644 G:A645, U:A593, U:A644, G:A646 3i1m A1549 Pout·4Bout A1653, A1654, N121, N123, N124, N125 A:A1360 A:A1360, G:A1361, C:A979, C:A980 1vs5 A1549 Pout·4Bout A1629, A1630, A1631, A1632, A1633, A1634 U:A644 G:A645, U:A593, U:A644, G:A646 2z4k A1549 Pout·4Bout A1629, A1630, A1631, A1632, A1633, A1634 U:A644 G:A645, U:A593, U:A644, G:A646 3i1s A1558 Pout·4Bout A1708, A1709, A1710, A1711, A1712 A:A1349 A:A1350, G:A1371, U:A1372, G:A1370 3ora A1561 Pout·4Bout A1712, A1713, A1714, A1715, A1716 A:A1349 U:A1351, G:A1371, U:A1372, G:A1370 2i2p A1562 Pout·4Bout A1697, A1698, A1699, A1700, A1701, A1702 G:A266 G:A257, G:A259, G:A258, U:A268 2z4k A1562 Pout·4Bout A1689, A1690, A1691, A1692, A1693 A:A1201 G:A1050, G:A1207, C:A1208, U:A1205 2qbj A1562 Pout·4Bout A1693, A1694, A1695, A1696, A1697, A1698 U:A644 G:A592, U:A593, G:A646, G:A645 2z4m A1563 Pout·4Bout A1692, A1693, A1694, A1695, A1696, A1697 U:A644 G:A592, U:A593, G:A646, G:A645 4tou A1604 Pout·4Bout A1716, A1717, A1718, A1719, A1720, A1721 A:A415 G:A416, G:A417, C:A418, G:A425 4pea A1605 Pout·4Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259, C:A267 4tp6 A1605 Pout·4Bout A1718, A1719, A1720, A1721, A1722, A1723 G:A266 G:A257, G:A258, G:A259, C:A267

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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