MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs8:B2932, See in JSmolClick on the image to toggle views Site type: 3Pout Schematic drawing for 3Pout List of all 207 Mg2+ binding sites with the site type 3Pout 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 5 of 9 | « 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 4bpo A5053 3Pout A2181, A2182, A2183, A2416, A2417, A2418 C:A978, A:A979, G:A980 4bpo A5004 3Pout A2111, A2112, A2113, A2213, A2326, A2327 C:A567, A:A1111, G:A568 4bpo A5054 3Pout A2160, A2184, A2185, A2419, A2420, A2421 U:A881, G:A986, U:A987 4bpo A5005 3Pout A2003, A2004, A2005, A2006, A2007, A2328 U:A8, U:A9, A:A11 4bpp A5075 3Pout A8211, A8212, A8213, A8214, A8215, A8216 G:A1399, G:A1400, C:A1246 4bpp A5037 3Pout A7603, A7604, A7605, A7606, A7607, A7608 G:A353, G:A368, G:A354 4bpp A5038 3Pout A7619, A7620, A7621, A7622, A7623, A7624 C:A1039, C:A1023, U:A1022 4bpp A5049 3Pout A7795, A7796, A7797, A7798, A7799, A7800 A:A283, U:A114, A:A115 4bpp A5004 3Pout A7075, A7076, A7077, A7078, A7079, A7080 G:A568, C:A567, A:A1111 4bpp A5005 3Pout A7091, A7092, A7093, A7094, A7095, A7096 U:A9, A:A11, U:A8 4bpp A5054 3Pout A7875, A7876, A7877, A7878, A7879, A7880 G:A986, U:A987, U:A881 4bpp A5053 3Pout A7859, A7860, A7861, A7862, A7863, A7864 G:A980, C:A978, A:A979 4dh9 A1884 3Pout A2117, A2118, Y317, Y318 G:A15, A:A16, U:A13 4dha A3799 3Pout A5080, A5081, A5082, A5083, A5084, A5085 C:A976, C:A982, G:A977 4dha A3734 3Pout A4843, A4844, A4845, A4846, R304 G:A2838, A:A2820, G:A2819 4dha A3810 3Pout A5126, A5127, A5128, A5129, A5130 A:A735, C:A1636, G:A1635 4dhc A3579 3Pout A4385, A4386, A4387, A4388, A4389 C:A1370, U:A773, G:A1356 4dr1 A1654 3Pout A2002, A2003, A2004, A2005 G:A15, A:A16, U:A13 4dr2 A1681 3Pout A2180, A2181, A2182, A2183 G:A15, A:A16, U:A13 4dr4 A1626 3Pout A2018, A2019, A2020, A2021 U:A652, G:A752, C:A651 4dr4 A1943 3Pout A2410, A2411, A2412, A2413, A2414 C:A643, G:A592, U:A591 4dr5 A1814 3Pout A2274, A2275, A2276, A2277, A2278, A2279 C:A934, U:A1345, A:A1346 4dr7 A1613 3Pout A2033, A2034, A2035, A2036, D401 G:A617, C:A620, A:A621 4dr7 A1715 3Pout A2282, A2283, A2284, A2285 A:A946, G:A945, G:A944 4dr7 A1651 3Pout A2129, A2130, A2131, A2132 G:A15, A:A16, U:A13

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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