MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df3:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·3Bout Schematic drawing for 2Pout·3Bout List of all 199 Mg2+ binding sites with the site type 2Pout·3Bout 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 8 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1vs8 B2927 2Pout·3Bout B3124, B3125, B3126, B3127, B3128, B3129 A:B616, G:B617 G:B617, G:B618, G:B619 1yi2 08071 2Pout·3Bout 04108, 06035, 07392, 07524, 07795, 07796 A:01815, C:01816 U:01813, C:01818, U:01817 1yij 08071 2Pout·3Bout 04127, 06056, 07408, 07537, 07808, 07809 A:01815, C:01816 U:01813, C:01818, U:01817 1yjn 08071 2Pout·3Bout 04128, 06069, 07418, 07549, 07821, 07822 A:01815, C:01816 U:01813, C:01818, U:01817 1yls B245 2Pout·3Bout B373, B374, B375, B376, B377, B378 A:B206, G:B205 A:B206, G:B205, G:B207 1yls D342 2Pout·3Bout D399, D400, D401, D402, D403, D404 C:D215, G:D216 G:D217, G:D227, G:D216 2avy A1545 2Pout·3Bout A1613, A1614, A1615, A1616, A1617, A1618 G:A803, U:A804 U:A772, G:A773, G:A771 2aw4 B2957 2Pout·3Bout B3262, B3263, B3264, B3265, B3266, B3267 A:B616, G:B617 G:B617, G:B618, G:B619 2aw4 B2923 2Pout·3Bout B3101, B3102, B3103, B3104, B3105, B3106 U:B29, A:B447 G:B474, U:B29, G:B30 2aw7 A1546 2Pout·3Bout A1617, A1618, A1619, A1620, A1621, A1622 G:A803, U:A804 U:A772, G:A773, G:A771 2awb B2927 2Pout·3Bout B3125, B3126, B3127, B3128, B3129, B3130 G:B617, A:B616 G:B617, G:B618, G:B619 2i2p X57 2Pout·3Bout A1877, A1878, X341, X342, X344, X346 G:X3, U:X2 C:A1399, G:A1401, G:X3 2i2p A1597 2Pout·3Bout A1866, A1867, A1868, A1869, A1870 C:A110, G:A111 G:A112, G:A111, G:A113 2i2t B2923 2Pout·3Bout B3111, B3112, B3113, B3114, B3115, B3116 U:B29, A:B447 G:B474, U:B29, G:B30 2i2t B3001 2Pout·3Bout B3461, B3462, B3463, B3464, B3465, B3466 A:B1000, A:B1001 G:B1003, G:B1002, C:B1153 2i2t B2983 2Pout·3Bout B3394, B3395, B3396, B3397, B3398, B3399 A:B2453, C:B2452 A:B2453, A:B2497, G:B2454 2nz4 Q9007 2Pout·3Bout F33, F35, Q9013, Q9014, Q9015, Q9016 C:Q52, G:Q53 G:Q54, A:Q28, G:Q53 2otl 08071 2Pout·3Bout 04130, 06070, 07417, 07550, 07818, 07819 A:01815, C:01816 U:01813, U:01817, C:01818 2qam B3309 2Pout·3Bout B3863, B3864, B3865, B3866, B3867, B3868 A:B616, G:B617 G:B617, G:B618, G:B619 2qb9 A2014 2Pout·3Bout A2370, A2371, A2372, A2373, A2374, A2375 G:A803, U:A804 U:A772, G:A773, G:A771 2qb9 A2044 2Pout·3Bout A2395, A2396, A2397, A2398, A2399, A2400 A:A315, A:A329 G:A319, A:A320, G:A318 2qbb A2016 2Pout·3Bout A2382, A2383, A2384, A2385, A2386, A2387 G:A803, U:A804 U:A772, G:A773, G:A771 2qbc B3133 2Pout·3Bout B3729, B3730, B3731, B3732, B3733, B3734 A:B616, G:B617 G:B618, G:B619, G:B617 2qbe B3309 2Pout·3Bout B3863, B3864, B3865, B3866, B3867, B3868 A:B616, G:B617 G:B617, G:B618, G:B619 2qbg B2927 2Pout·3Bout B3126, B3127, B3128, B3129, B3130, B3131 A:B616, G:B617 G:B617, G:B618, G:B619

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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