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 1 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 1vs5 A1600 2Pout·2Bout A1878, A1879, A1880, A1881, A1882, A1883 G:A258, G:A259 G:A259, G:A260 1vs6 B2957 2Pout·2Bout B3266, B3267, B3268, B3269, B3270, B3271 A:B616, G:B617 G:B617, G:B618 1vs6 B2937 2Pout·2Bout B3174, B3175, B3176, B3177, B3178, B3179 G:B649, C:B650 C:B650, G:B651 1vs6 B3001 2Pout·2Bout B3456, B3457, B3458, B3459, B3460, B3461 A:B1000, A:B1001 G:B1003, G:B1002 1vs7 A1566 2Pout·2Bout A1712, A1713, A1714, A1715, A1716, A1717 A:A1046, G:A1047 G:A1048, G:A1047 1vs8 B2907 2Pout·2Bout B3025, B3026, B3027, B3028, B3029, B3030 G:B831, U:B568 A:B945, A:B2448 1vt2 A2921 2Pout·2Bout A3127, A3128, A3129, A3130, A3131, A3132 A:A616, A:A608 G:A618, G:A619 1yjn 08100 2Pout·2Bout 03782, 04270, 05525, 06169, 07837, 07838 U:02078, C:02077 G:02079, G:02080 1yls B242 2Pout·2Bout B355, B356, B357, B358, B359, B360 C:B215, G:B216 G:B216, G:B217 2avy A1599 2Pout·2Bout A1874, A1875, A1876, A1877, A1878, A1879 G:A258, G:A259 G:A259, G:A260 2aw4 B2937 2Pout·2Bout B3171, B3172, B3173, B3174, B3175, B3176 G:B649, C:B650 C:B650, G:B651 2aw4 B3001 2Pout·2Bout B3452, B3453, B3454, B3455, B3456, B3457 A:B1000, A:B1001 G:B1003, G:B1002 2aw7 A1565 2Pout·2Bout A1713, A1714, A1715, A1716, A1717, A1718 A:A1046, G:A1047 G:A1048, G:A1047 2i2p A1550 2Pout·2Bout A1639, A1640, A1641, A1642, A1643, A1644 A:A315, U:A317 G:A318, G:A319 2i2p A1598 2Pout·2Bout A1871, A1872, A1873, A1874, A1875, A1876 A:A918, A:A1394 A:A918, A:A919 2i2u A1581 2Pout·2Bout A1778, A1779, A1780, A1781, A1782 A:A937, C:A936 C:A1344, G:A1343 2i2v B3020 2Pout·2Bout B3537, B3538, B3539, B3540, B3541, 41054 A:B2741, A:B2740 G:B2742, U:B2743 2i2v B3016 2Pout·2Bout B3523, B3524, B3525, B3526, C1034, C1036 A:B1791, C:B1790 U:B1827, G:B1828 2qal A2014 2Pout·2Bout A2015, A2016, A2017, A2018, A2019, A2020 U:A804, G:A803 U:A772, G:A771 2qal A2342 2Pout·2Bout A2343, A2344, A2345, A2346, A2347, A2348 G:A259, G:A258 G:A259, G:A260 2qam B3543 2Pout·2Bout B4053, B4054, B4055, B4056, B4057, B4058 A:B1000, A:B1001 G:B1003, G:B1002 2qam B3521 2Pout·2Bout B4035, B4036, B4037, B4038, B4039, B4040 U:B686, C:B687 G:B771, G:B770 2qan A2346 2Pout·2Bout A2347, A2348, A2349, A2350, A2351, A2352 A:A1394, A:A918 A:A918, A:A919 2qan A2353 2Pout·2Bout A2354, A2355, A2356, A2357, A2358, A2359 G:A259, G:A258 G:A259, G:A260 2qan A2340 2Pout·2Bout A2341, A2342, A2343, A2344, A2345 C:A110, G:A111 G:A111, G:A112

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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