MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2288, See in JSmolClick on the image to toggle views Site type: 4Bout Schematic drawing for 4Bout List of all 105 Mg2+ binding sites with the site type 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 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1egk C13 4Bout C87, C88, C90, C91, C92, D89 U:C115, G:C116, DA:D126, DG:D124 1hr2 A20 4Bout A365, A366, A367, A368, A369, A370 U:A144, U:A156, U:A157, G:A158 3ivk C122 4Bout C138, C139, C140, C141, C142, C143 A:C97, G:C91, G:C92, U:C93 2g91 A191 4Bout A116, A120, A162, A180, A184, B122 G:A4, C:A5, U:A3, U:B12 2g91 B192 4Bout A139, A140, B138, B141 G:A2, U:A3, G:B15, C:B14 4a17 0203 4Bout 07043, 07044, 07045, 07046, 07047, 07048 U:396, G:397, U:395, U:379 3v2f B210 4Bout B328, B329, B330, B331, B332 U:B80, G:B98, U:B96, G:B97 3v27 B222 4Bout B347, B348, B349, B350, B351, B352 U:B80, U:B96, G:B97, G:B98 1yls B243 4Bout A361, A366, B362, B363, B364, B365 G:A108, G:B202, G:B203, G:B201 1ehz A510 4Bout A712, A713, A714, A715, A716 G:A3, G:A4, U:A68, U:A69 2nug F513 4Bout E522, F542, F543, F544, F545, F552 G:E26, G:F26, U:E25, U:F25 3i1z A1543 4Bout A1621, A1622, A1623, A1624, A1625, A1626 G:A646, G:A592, U:A593, G:A645 3ofa A1543 4Bout A1620, A1621, A1622, A1623, A1624, A1625 G:A646, G:A592, U:A593, G:A645 3ofo A1543 4Bout A1619, A1620, A1621, A1622, A1623, A1624 G:A646, G:A592, U:A593, G:A645 2qp0 A1590 4Bout A2113, A2114, A2115, A2116, A2117 G:A1048, G:A1050, G:A1207, C:A1208 4tol A1610 4Bout A1744, A1745, A1746, A1747, A1748, A1749 G:A646, U:A593, U:A594, G:A645 4tp8 A1610 4Bout A1743, A1744, A1745, A1746, A1747, A1748 G:A646, U:A593, U:A594, G:A645 4gd2 A1620 4Bout A1792, A1793, A1794, A1795, A1796, A1797 G:A645, G:A592, U:A593, G:A646 4gd1 A1636 4Bout A1867, A1868, A1869, A1870, A1871, U101 G:A1525, C:A1524, G:A1526, C:A1509 4ji8 A1680 4Bout A2138, N201, N202, N203 A:A1360, G:A1361, C:A980, C:A979 4ji5 A1714 4Bout A2010, A2011, A2012, A2013, A2014, A2015 G:A44, U:A45, G:A396, C:A395 4ji1 A1723 4Bout A2028, A2029, A2030, A2031, A2032, A2033 G:A854, U:A833, G:A852, G:A853 4ji1 A1737 4Bout A2111, A2112, A2113, A2114, A2115, A2116 G:A494, G:A492, G:A490, G:A491 4dv1 A1764 4Bout A2091, A2092, A2093, A2094, A2095, A2096 G:A664, G:A741, G:A742, G:A666 4dv0 A1780 4Bout A2103, A2104, A2105, A2106 G:A664, G:A666, U:A740, G:A741

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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