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 3 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 3v2d A3373 4Bout A4736, A4737, A4738, A4739, A4740 U:A2457, G:A2494, G:A2495, G:A2455 3v2f A3276 4Bout A4191, A4192, A4193, A4194, A4195, A4196 G:A79, G:A80, G:A82, G:A81 3v2f B210 4Bout B328, B329, B330, B331, B332 U:B80, G:B98, U:B96, G:B97 3v2f A3215 4Bout A3978, A3979, A3980, A3981, A3982 G:A2494, G:A2455, G:A2495, U:A2457 4a17 0203 4Bout 07043, 07044, 07045, 07046, 07047, 07048 U:396, G:397, U:395, U:379 4bpn A5043 4Bout A6110, A6111, A6112, A6113, A6114, A6115 G:A1614, A:A1708, U:A1711, G:A1710 4bpo A5009 4Bout A2103, A2105, A2116, A2117, A2119, A2337 G:A550, C:A552, A:A579, G:A580 4bpo A5043 4Bout A2301, A2302, A2311, A2312, A2402, A2403 G:A1614, G:A1710, U:A1711, A:A1708 4bpp A5040 4Bout A7651, A7652, A7653, A7654, A7655, A7656 C:A86, U:A57, U:A84, G:A85 4bpp A5009 4Bout A7155, A7156, A7157, A7158, A7159, A7160 A:A579, G:A580, G:A550, C:A552 4bpp A5043 4Bout A7699, A7700, A7701, A7702, A7703, A7704 G:A1614, A:A1708, U:A1711, G:A1710 4bpp A5073 4Bout A8179, A8180, A8181, A8182, A8183, A8184 G:A1281, U:A1282, U:A1283, U:A1287 4dh9 A1894 4Bout A2143, A2144, A2145, A2146, A2147, A2148 G:A1419, G:A1480, U:A1481, G:A1482 4dha A3650 4Bout A4545, A4546, A4547, A4548, A4549 U:A534, G:A533, G:A558, G:A559 4dha A3612 4Bout A4414, A4415, A4416, A4417, A4418 G:A186, G:A187, G:A188, G:A189 4dr5 A1800 4Bout A2192, A2193, A2194, A2195, A2196, A2197 G:A595, G:A594, G:A593, G:A592 4dr7 A1788 4Bout A2302, A2303, A2304, A2305, A2306, A2307 G:A593, G:A594, G:A592, U:A646 4dv0 A1780 4Bout A2103, A2104, A2105, A2106 G:A664, G:A666, U:A740, G:A741 4dv1 A1764 4Bout A2091, A2092, A2093, A2094, A2095, A2096 G:A664, G:A741, G:A742, G:A666 4gar A3093 4Bout A3636, A3637, A3638, A3639, A3640, A3641 G:A1464, G:A1465, U:A1466, C:A1446 4gd1 A1636 4Bout A1867, A1868, A1869, A1870, A1871, U101 G:A1525, C:A1524, G:A1526, C:A1509 4gd2 A1620 4Bout A1792, A1793, A1794, A1795, A1796, A1797 G:A645, G:A592, U:A593, G:A646 4ji1 A1796 4Bout A2467, A2468, A2469, A2470, A2471, A2472 G:A44, G:A396, U:A45, 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

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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