MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbe:B3457, See in JSmolClick on the image to toggle views Site type: 2Pout·4Bout Schematic drawing for 2Pout·4Bout List of all 68 Mg2+ binding sites with the site type 2Pout·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 1 of 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1vs6 B2922 2Pout·4Bout B3098, B3099, B3100, B3101, B3102, B3103 A:B2009, U:B1267 G:B2010, U:B2011, G:B2012, A:B2009 1vs8 B2930 2Pout·4Bout B3139, B3140, B3141, B3142, B3143, B3144 C:B2452, A:B2453 A:B2453, G:B2454, A:B2497, G:B2455 1vt2 A3003 2Pout·4Bout A3509, A3510, A3511, A3512, A3513 A:A2705, C:A2704 A:A2705, A:A2706, U:A2701, U:A2707 2i2t B3016 2Pout·4Bout B3523, B3524, B3525, B3526, C278, C279 C:B1790, A:B1791 G:B1826, U:B1827, G:B1792, G:B1828 2otj 08071 2Pout·4Bout 04142, 06085, 07434, 07562, 07831, 07832 A:01815, C:01816 A:01759, U:01813, C:01818, U:01817 2qal A2031 2Pout·4Bout A2032, A2033, A2034, A2035, A2036, A2037 G:A645, U:A644 G:A645, U:A593, U:A644, G:A646 2qam B3457 2Pout·4Bout B3985, B3986, B3987, B3988, B3989, B3990 A:B2451, C:B2452 A:B2497, G:B2455, A:B2453, G:B2454 2qao B3152 2Pout·4Bout B3743, B3744, B3745, B3746, B3747, B3748 A:B2453, C:B2452 A:B2453, G:B2454, A:B2497, G:B2455 2qb9 A2031 2Pout·4Bout A2384, A2385, A2386, A2387, A2388, A2389 G:A645, U:A644 G:A645, U:A593, U:A644, G:A646 2qba B3457 2Pout·4Bout B3982, B3983, B3984, B3985, B3986, B3987 A:B2451, C:B2452 A:B2453, G:B2454, A:B2497, G:B2455 2qbc B3152 2Pout·4Bout B3745, B3746, B3747, B3748, B3749, B3750 C:B2452, A:B2453 A:B2453, G:B2454, A:B2497, G:B2455 2qbe B3457 2Pout·4Bout B3982, B3983, B3984, B3985, B3986, B3987 A:B2451, C:B2452 A:B2497, G:B2455, A:B2453, G:B2454 2qbh A1548 2Pout·4Bout A1629, A1630, A1631, A1632, A1633, A1634 G:A645, U:A644 G:A645, U:A593, U:A644, G:A646 2qbk B2930 2Pout·4Bout B3141, B3142, B3143, B3144, B3145, B3146 A:B2453, C:B2452 A:B2453, G:B2454, A:B2497, G:B2455 2qou A1548 2Pout·4Bout A1922, A1923, A1924, A1925, A1926, A1927 G:A645, U:A644 G:A645, U:A593, U:A644, G:A646 3cc2 08071 2Pout·4Bout 03670, 05625, 06994, 07126, 07398, 07399 A:01815, C:01816 A:01759, U:01813, C:01818, U:01817 3i1p A2980 2Pout·4Bout A3397, A3398, A3399, A3400, A3401, A3402 G:A2454, A:A2453 G:A2455, C:A2496, G:A2454, A:A2453 3i1t A2978 2Pout·4Bout A3389, A3390, A3391, A3392, A3393, A3394 U:A2387, A:A2386 C:A2326, A:A2386, G:A2389, U:A2387 3i20 A2974 2Pout·4Bout A3369, A3370, A3371, A3372, A3373, A3374 A:A2453, C:A2452 A:A2497, G:A2454, G:A2455, A:A2453 3i21 A1553 2Pout·4Bout A1681, A1682, A1683, A1684, A1685, A1686 C:A797, A:A781 U:A798, G:A799, G:A800, C:A797 3i22 A2919 2Pout·4Bout A3115, A3116, A3117, A3118, A3119, A3120 C:A1257, G:A579 U:A580, C:A581, U:A1258, G:A1259 3oas A2979 2Pout·4Bout A3398, A3399, A3400, A3401, A3402, A3403 G:A2454, A:A2453 G:A2455, C:A2496, G:A2454, A:A2453 3oat A2905 2Pout·4Bout A3044, A3045, A3046, A3047, A3048, A3049 U:A29, A:A447 G:A473, G:A474, U:A29, G:A30 3ofc A2905 2Pout·4Bout A3045, A3046, A3047, A3048, A3049, A3050 U:A29, A:A447 G:A473, G:A474, U:A29, G:A30 3ofq A3003 2Pout·4Bout A3504, A3505, A3506, A3507, A3508 A:A2705, C:A2704 A:A2705, A:A2706, U:A2701, U:A2707

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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