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 3 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 4dr6 A1705 Pout·4Bout A2256, A2257, A2258, N201 A:A1360 C:A980, C:A979, A:A1360, G:A1361 3v26 A1711 Pout·4Bout A1947, A1948, A1949, A1950, A1951, A1952 C:A398 C:A36, U:A37, G:A35, G:A548 4dr2 A1751 Pout·4Bout A2388, A2389, A2390, A2391 A:A1360 C:A980, C:A979, A:A1360, G:A1361 4dv1 A1810 Pout·4Bout A2206, A2207, A2208, A2209, A2210, A2211 A:A766 U:A813, C:A811, C:A812, A:A767 4dr5 A1817 Pout·4Bout A2292, A2293, A2294, A2295, A2296, A2297 G:A1057 G:A1058, U:A1199, C:A1059, G:A1198 4duz A1827 Pout·4Bout A2188, A2189, A2190, A2191, A2192 A:A766 U:A813, C:A812, A:A768, C:A811 4dv5 A1829 Pout·4Bout A2188, A2189, A2190, A2191, A2192, A2193 A:A766 C:A812, U:A813, A:A767, C:A811 4dv3 A1835 Pout·4Bout A2191, A2192, A2193, A2194, A2195, A2196 A:A766 A:A767, C:A812, A:A768, C:A811 4ji6 A1839 Pout·4Bout A2330, A2658, A2659, A2660, A2661, A2662 G:A1057 C:A1059, G:A1198, G:A1058, U:A1199 4dv7 A1846 Pout·4Bout A2201, A2202, A2203, A2204, A2205, A2206 A:A766 U:A813, C:A812, A:A767, C:A811 4dv3 A1852 Pout·4Bout A2235, A2236, A2237, A2238, A2239 G:A266 G:A257, G:A266, U:A256, A:A270 4dh9 A1870 Pout·4Bout A2091, A2092, A2093, A2094 A:A583 G:A584, G:A585, C:A756, U:A757 4ji8 A1872 Pout·4Bout A2754, A2755, A2756, A2757, A2758, A2759 G:A1057 C:A1059, G:A1198, U:A1199, G:A1058 4dr4 A1942 Pout·4Bout A2404, A2405, A2406, A2407, A2408, A2409 A:A642 G:A595, G:A594, G:A593, G:A592 2qal A2115 Pout·4Bout A2116, A2117, A2118, A2119, A2120, A2121 G:A266 G:A257, U:A268, G:A258, G:A259 2qal A2129 Pout·4Bout A2130, A2131, A2132, A2133, A2134, A2135 A:A559 U:A24, G:A9, A:A10, A:A559 2qan A2141 Pout·4Bout A2142, A2143, A2144, A2145, A2146, A2147 G:A266 G:A257, G:A258, U:A268, G:A259 3i1p A2919 Pout·4Bout A3118, A3119, A3120, A3121, A3122, A3123 C:A1257 U:A580, C:A581, G:A1259, U:A1258 2qbi B2922 Pout·4Bout B3096, B3097, B3098, B3099, B3100, B3101 U:B1267 G:B2010, U:B2011, G:B2012, A:B2009 2qbk B2923 Pout·4Bout B3106, B3107, B3108, B3109, B3110, B3111 U:B1267 A:B2009, U:B2011, G:B2012, G:B2010 2qox B2923 Pout·4Bout B3104, B3105, B3106, B3107, B3108, B3109 U:B1267 U:B2011, G:B2012, G:B2010, A:B2009 1vs8 B2923 Pout·4Bout B3105, B3106, B3107, B3108, B3109, B3110 U:B1267 U:B2011, G:B2012, G:B2010, A:B2009 2i2v B2923 Pout·4Bout B3115, B3116, B3117, B3118, B3119, B3120 U:B1267 U:B2011, G:B2012, G:B2010, A:B2009 2qbg B2923 Pout·4Bout B3107, B3108, B3109, B3110, B3111, B3112 U:B1267 U:B2011, G:B2012, A:B2009, G:B2010 2awb B2923 Pout·4Bout B3106, B3107, B3108, B3109, B3110, B3111 U:B1267 U:B2011, G:B2012, G:B2010, A:B2009

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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