MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbd:A2328, See in JSmolClick on the image to toggle views Site type: 3Pout·2Bout Schematic drawing for 3Pout·2Bout List of all 131 Mg2+ binding sites with the site type 3Pout·2Bout 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 1dfu N504 3Pout·2Bout M536, N507, N527, N528, N530, N568 A:M99, G:N75, U:N74 G:N76, G:N75 1l2x A38 3Pout·2Bout A39, A40, A41, A42, A43, A44 C:A26, G:A27, G:A28 G:A27, G:A28 1vs6 B2931 3Pout·2Bout B3143, B3144, B3145, B3146, B3147, B3148 A:B1937, A:B1936, G:B1959 G:B1959, A:B1960 1vs6 B2953 3Pout·2Bout B3245, B3246, B3247, B3248, B3249, B3250 C:B944, G:B831, U:B568 A:B945, A:B2448 1vs7 A1602 3Pout·2Bout A1886, A1887, A1888, A1889, A1890, A1891 A:A1394, G:A917, A:A918 A:A918, A:A919 1vs8 B2985 3Pout·2Bout B3405, B3406, B3407, B3408, B3409, B3410 C:B2050, A:B2051, G:B2578 A:B2051, A:B2614 1vt2 A2968 3Pout·2Bout A3343, A3344, A3345, A3346, A3347, A3348 A:A2051, G:A2578, C:A2050 A:A2051, A:A2614 2aw4 B2953 3Pout·2Bout B3241, B3242, B3243, B3244, B3245, L345 C:B944, G:B831, U:B568 A:B945, A:B2448 2aw7 A1601 3Pout·2Bout A1888, A1889, A1890, A1891, A1892, A1893 A:A1394, G:A917, A:A918 A:A918, A:A919 2awb B2907 3Pout·2Bout B3026, B3027, B3028, B3029, B3030, B3031 G:B831, U:B568, C:B944 A:B945, A:B2448 2awb B2986 3Pout·2Bout B3406, B3407, B3408, B3409, B3410, B3411 C:B2050, A:B2051, G:B2578 A:B2051, A:B2614 2i2t B2953 3Pout·2Bout B3252, B3253, B3254, B3255, B3256, L455 C:B944, G:B831, U:B568 A:B945, A:B2448 2i2u A1596 3Pout·2Bout A1856, A1857, A1858, A1859, X267, X270 G:A1401, U:X2, G:X3 C:A1399, G:A1401 2i2u A1574 3Pout·2Bout A1745, A1746, A1747, A1748, A1749, A1750 A:A1394, G:A917, A:A918 A:A918, A:A919 2i2v B2907 3Pout·2Bout B3035, B3036, B3037, B3038, B3039, B3040 C:B944, U:B568, G:B831 A:B945, A:B2448 2i2v B2909 3Pout·2Bout B3045, B3046, B3047, B3048, B3049, B3050 A:B1936, A:B1937, G:B1959 G:B1959, A:B1960 2qal A2044 3Pout·2Bout A2045, A2046, A2047, A2048, A2049, A2050 A:A315, U:A317, C:A316 G:A319, G:A318 2qam B3282 3Pout·2Bout B3840, B3841, B3842, B3843, B3844, B3845 C:B944, G:B831, U:B568 A:B945, A:B2448 2qam B3157 3Pout·2Bout B3738, B3739, B3740, B3741, B3742, B3743 A:B1937, A:B1936, G:B1959 A:B1960, G:B1959 2qao B3014 3Pout·2Bout B3630, B3631, B3632, B3633, B3634, L145 U:B568, G:B831, C:B944 A:B945, A:B2448 2qba B3282 3Pout·2Bout B3842, B3843, B3844, B3845, B3846, B3847 C:B944, G:B831, U:B568 A:B945, A:B2448 2qbc B3014 3Pout·2Bout B3631, B3632, B3633, B3634, B3635, L145 U:B568, G:B831, C:B944 A:B945, A:B2448 2qbd A2328 3Pout·2Bout A2329, A2330, A2331, A2332, A2333, A2334 A:A918, A:A1394, G:A917 A:A918, A:A919 2qbd A2164 3Pout·2Bout A2165, A2166, A2167, A2168, A2169 A:A768, U:A804, A:A767 A:A768, G:A769 2qbf A1600 3Pout·2Bout A1886, A1887, A1888, A1889, A1890, A1891 A:A1394, G:A917, A:A918 A:A918, A:A919

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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