MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3382, See in JSmolClick on the image to toggle views Site type: 4Pout·Bout Schematic drawing for 4Pout·Bout List of all 125 Mg2+ binding sites with the site type 4Pout·Bout 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 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qp1 B2910 4Pout·Bout B3548, B3549, B3550, B3551, B3552, B3553 A:B1987, C:B1986, C:B2551, A:B1669 G:B1954 2z4l B2936 4Pout·Bout B3160, B3161, B3162, B3163, B3164, B3165 U:B2613, C:B2050, A:B2051, G:B2578 A:B2614 2z4l B2971 4Pout·Bout B3324, B3325, B3326, B3327, B3328, B3329 A:B1669, C:B1986, A:B1987, C:B2551 G:B1954 2z4n B2911 4Pout·Bout B3043, B3044, B3045, B3046, B3047, B3048 C:B2551, A:B1987, A:B1669, C:B1986 G:B1954 3df2 B3181 4Pout·Bout B4182, B4183, B4184, B4185, B4186, B4187 U:B2613, C:B2050, A:B2051, G:B2578 A:B2614 3df2 B3382 4Pout·Bout B4383, B4384, B4385, B4386, B4387, B4388 A:B1669, C:B1986, C:B2551, A:B1987 G:B1954 3df4 B3033 4Pout·Bout B4034, B4035, B4036, B4037, B4038, B4039 C:B1986, C:B2551, A:B1669, A:B1987 G:B1954 3df4 B3026 4Pout·Bout B4027, B4028, B4029, B4030, B4031, B4032 A:B1937, A:B1936, C:B1958, G:B1959 G:B1959 3i1n A2947 4Pout·Bout A3243, A3244, A3245, A3246, A3247, A3248 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377 3i1n A2954 4Pout·Bout A3275, A3276, A3277, A3278, A3279, A3280 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954 3i1p A2956 4Pout·Bout A3279, A3280, A3281, A3282, A3283, A3284 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954 3i1p A2949 4Pout·Bout A3247, A3248, A3249, A3250, A3251, A3252 C:A1351, C:A1376, U:A1352, G:A1377 G:A1377 3i1r A2954 4Pout·Bout A3272, A3273, A3274, A3275, A3276, A3277 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954 3i1r A2947 4Pout·Bout A3240, A3241, A3242, A3243, A3244, A3245 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377 3i1t A2956 4Pout·Bout A3282, A3283, A3284, A3285, A3286, A3287 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954 3i1t A2949 4Pout·Bout A3250, A3251, A3252, A3253, A3254, A3255 C:A1351, C:A1376, U:A1352, G:A1377 G:A1377 3i20 A2947 4Pout·Bout A3241, A3242, A3243, A3244, A3245, A3246 C:A1351, U:A1352, G:A1377, C:A1376 G:A1377 3i20 A2954 4Pout·Bout A3273, A3274, A3275, A3276, A3277, A3278 A:A1669, C:A1986, A:A1987, C:A2551 G:A1954 3i22 A2947 4Pout·Bout A3244, A3245, A3246, A3247, A3248 C:A1314, G:A1332, G:A1334, U:A1313 C:A1335 3mut R671 4Pout·Bout R715, R716, R717, R718, R719, R720 U:R53, U:R81, C:R52, C:R44 A:R82 3oas A2948 4Pout·Bout A3248, A3249, A3250, A3251, A3252, A3253 C:A1351, C:A1376, U:A1352, G:A1377 G:A1377 3oas A2955 4Pout·Bout A3280, A3281, A3282, A3283, A3284, A3285 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954 3oat A2953 4Pout·Bout A3264, A3265, A3266, A3267, A3268, A3269 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954 3ofc A2952 4Pout·Bout A3266, A3267, A3268, A3269, A3270, A3271 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954 3ofd A2955 4Pout·Bout A3278, A3279, A3280, A3281, A3282, A3283 A:A1669, C:A1986, C:A2551, A:A1987 G:A1954

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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