MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·2Bout Schematic drawing for 2Pout·2Bout List of all 279 Mg2+ binding sites with the site type 2Pout·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 2 of 12 | « 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 2qan A2346 2Pout·2Bout A2347, A2348, A2349, A2350, A2351, A2352 A:A1394, A:A918 A:A918, A:A919 2qan A2121 2Pout·2Bout A2122, A2123, A2124, A2125, A2126, A2127 A:A315, U:A317 G:A319, G:A318 2qb9 A2077 2Pout·2Bout A2422, A2423, A2424, A2425, A2426, A2427 G:A1047, A:A1046 G:A1047, G:A1048 2qba B3543 2Pout·2Bout B4050, B4051, B4052, B4053, B4054, B4055 A:B1000, A:B1001 G:B1003, G:B1002 2qbb A2121 2Pout·2Bout A2467, A2468, A2469, A2470, A2471, A2472 A:A315, U:A317 G:A319, G:A318 2qbb A2346 2Pout·2Bout A2653, A2654, A2655, A2656, A2657, A2658 A:A1394, A:A918 A:A918, A:A919 2qbd A2014 2Pout·2Bout A2015, A2016, A2017, A2018, A2019, A2020 U:A804, G:A803 U:A772, G:A771 2qbe B3543 2Pout·2Bout B4049, B4050, B4051, B4052, B4053, B4054 A:B1000, A:B1001 G:B1002, G:B1003 2qbe B3521 2Pout·2Bout B4031, B4032, B4033, B4034, B4035, B4036 U:B769, G:B770 G:B770, U:B769 2qbf A1563 2Pout·2Bout A1699, A1700, A1701, A1702, A1703, A1704 A:A329, A:A315 G:A319, A:A320 2qbi B3001 2Pout·2Bout B3451, B3452, B3453, B3454, B3455, B3456 A:B1000, A:B1001 G:B1002, G:B1003 2qbj A1546 2Pout·2Bout A1617, A1618, A1619, A1620, A1621, A1622 G:A803, U:A804 G:A771, U:A772 2qbj A1601 2Pout·2Bout A1889, A1890, A1891, T355, T356, T358 G:A259, G:A258 G:A259, G:A260 2qov B2946 2Pout·2Bout B3209, B3210, B3211, B3212, B3213 A:B2311, C:B2310 G:B2304, U:B2302 2qov B3001 2Pout·2Bout B3455, B3456, B3457, B3458, B3459, B3460 A:B1000, A:B1001 G:B1003, G:B1002 2qoy A1545 2Pout·2Bout A1910, A1911, A1912, A1913, A1914, A1915 U:A804, G:A803 U:A772, G:A771 2qoz B3001 2Pout·2Bout B3946, B3947, B3948, B3949, B3950, B3951 A:B1000, A:B1001 G:B1002, G:B1003 2qoz B2953 2Pout·2Bout B3736, B3737, B3738, B3739, B3740, L286 G:B831, C:B944 A:B945, A:B2448 2qp0 A1595 2Pout·2Bout A2140, A2141, A2142, A2143, A2144 U:A1348, A:A1349 G:A1370, U:A1351 2qp1 B2917 2Pout·2Bout B3582, B3583, B3584, B3585, B3586, B3587 A:B2033, G:B2027 U:B2028, G:B2029 2qp1 B2907 2Pout·2Bout B3533, B3534, B3535, B3536, B3537, L145 C:B944, G:B831 A:B945, A:B2448 2z4l B3002 2Pout·2Bout B3453, B3454, B3455, B3456, B3457, B3458 A:B1000, A:B1001 G:B1002, G:B1003 2z4l B2998 2Pout·2Bout B3435, B3436, B3437, B3438, B3439, B3440 U:B686, C:B687 G:B771, G:B770 2z4m A1564 2Pout·2Bout A1698, A1699, A1700, A1701, A1702, A1703 A:A315, A:A329 G:A319, G:A318 2z4m A1601 2Pout·2Bout A1884, A1885, A1886, A1887, A1888, A1889 A:A1394, 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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