MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3464, See in JSmolClick on the image to toggle views Site type: 3Bout Schematic drawing for 3Bout List of all 341 Mg2+ binding sites with the site type 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 6 of 14 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3hhn C1025 3Bout C1057, C1058, C1059, C1060, C1061, C1062 G:C87, G:C88, A:C103 3hhn E1024 3Bout E66, E1052, E1053, E1054, E1055, E1056 G:E75, A:E80, G:E81 3hhn C60 3Bout C59, C61, C62, C63, C64, C65 G:C81, A:C80, G:C75 3i1n A2995 3Bout A3467, A3468, A3469, A3470, A3471, A3472 G:A1410, U:A1411, A:A1590 3i1n A2998 3Bout A3483, A3484, A3485, A3486, A3487, A3488 G:A1465, U:A1466, G:A1464 3i1n A2919 3Bout A3118, A3119, A3120, A3121, A3122, A3123 G:A1259, U:A580, U:A1258 3i1o A1558 3Bout A1708, A1709, A1710, A1711, A1712 G:A1371, U:A1372, G:A1370 3i1p A2972 3Bout A3359, A3360, A3361, A3362, A3363, A3364 G:A2242, U:A2243, A:A2241 3i1r A2904 3Bout A3040, A3041, A3042, A3043, A3044, A3045 G:A17, U:A521, U:A18 3i1r A2919 3Bout A3117, A3118, A3119, A3120, A3121, A3122 U:A580, U:A1258, G:A1259 3i1t B119 3Bout B627, B628, B629, B630, B631 U:B80, U:B95, G:B96 3i1t A2930 3Bout A3167, A3168, A3169, A3170, E271, E276 G:A797, G:A798, C:A679 3i1t A2982 3Bout A3411, A3412, A3413, A3414, A3415, A3416 G:A2549, G:A2550, C:A2551 3i1z A1557 3Bout A1686, A1687, A1688, A1689, A1690, A1691 G:A800, U:A798, G:A799 3i20 A3005 3Bout A3520, A3521, A3522, A3523, A3524, A3525 C:A2047, G:A2048, G:A2049 3i20 A2998 3Bout A3482, A3483, A3484, A3485, A3486, A3487 G:A1465, U:A1466, G:A1464 3i20 A2904 3Bout A3040, A3041, A3042, A3043, A3044, A3045 U:A521, G:A17, U:A18 3i20 A2924 3Bout A3141, A3142, A3143, A3144, A3145, A3146 A:A756, A:A739, G:A757 3i20 A2919 3Bout A3117, A3118, A3119, A3120, A3121, A3122 G:A1259, U:A580, U:A1258 3i20 A3001 3Bout A3502, A3503, A3504, A3505, A3506, A3507 G:A1823, G:A1824, U:A1825 3i22 A2925 3Bout A3146, A3147, A3148, A3149, A3150, A3151 G:A757, A:A739, A:A756 3i22 A2923 3Bout A3136, A3137, A3138, A3139, A3140, A3141 C:A650, G:A638, G:A651 3ivk C129 3Bout C171, C172, C173, C174, C175, C176 G:C17, G:C18, U:C16 3ivk M125 3Bout M156, M157, M158, M159, M160, M161 A:M80, G:M81, G:M75 3ivk M124 3Bout M150, M151, M152, M153, M154, M155 G:M72, A:M73, G:M105

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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