MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbd:A2328, See in JSmolClick on the image to toggle views Site type: 3Pout·2Bout Schematic drawing for 3Pout·2Bout List of all 131 Mg2+ binding sites with the site type 3Pout·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 2 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qbg B2939 3Pout·2Bout B3188, B3189, B3190, B3191, B3192, B3193 A:B447, A:B28, U:B29 G:B473, G:B474 2qbg B2907 3Pout·2Bout B3027, B3028, B3029, B3030, B3031, B3032 C:B944, G:B831, U:B568 A:B945, A:B2448 2qbg B2909 3Pout·2Bout B3037, B3038, B3039, B3040, B3041, B3042 A:B1936, G:B1959, A:B1937 A:B1960, G:B1959 2qbi B2953 3Pout·2Bout B3242, B3243, B3244, B3245, B3246, L284 C:B944, G:B831, U:B568 A:B945, A:B2448 2qbi B3012 3Pout·2Bout B3495, B3496, B3497, B3498, B3499, B3500 G:B570, A:B973, U:B569 A:B820, A:B821 2qbj A1572 3Pout·2Bout A1755, A1756, A1757, A1758, A1759, A1760 A:A768, C:A805, A:A767 A:A768, G:A769 2qbj A1600 3Pout·2Bout A1883, A1884, A1885, A1886, A1887, A1888 A:A1394, G:A917, A:A918 A:A918, A:A919 2qbk B2907 3Pout·2Bout B3028, B3029, B3030, B3031, B3032, L145 U:B568, G:B831, C:B944 A:B945, A:B2448 2qbk B2909 3Pout·2Bout B3037, B3038, B3039, B3040, B3041, B3042 A:B1937, A:B1936, G:B1959 A:B1960, G:B1959 2qov B2931 3Pout·2Bout B3142, B3143, B3144, B3145, B3146, B3147 A:B1937, A:B1936, G:B1959 A:B1960, G:B1959 2qov B2953 3Pout·2Bout B3244, B3245, B3246, B3247, B3248, B3249 C:B944, G:B831, U:B568 A:B945, A:B2448 2qov B2905 3Pout·2Bout B3015, B3016, B3017, B3018, B3019 A:B802, G:B674, A:B675 U:B803, A:B804 2qox B2907 3Pout·2Bout B3026, B3027, B3028, B3029, B3030, L145 U:B568, C:B944, G:B831 A:B945, A:B2448 2qoy A1550 3Pout·2Bout A1935, A1936, A1937, A1938, A1939, A1940 A:A315, A:A329, C:A316 G:A318, G:A319 2qp0 A1560 3Pout·2Bout A1975, A1976, A1977, A1978, A1979, A1980 A:A768, C:A805, A:A767 A:A768, G:A769 2qp1 B2987 3Pout·2Bout B3917, B3918, B3919, B3920, B3921, B3922 G:B2578, U:B2613, A:B2051 A:B2051, A:B2614 2z4l B2932 3Pout·2Bout B3141, B3142, B3143, B3144, B3145, B3146 A:B1937, A:B1936, G:B1959 A:B1960, G:B1959 2z4l B2954 3Pout·2Bout B3242, B3243, B3244, B3245, B3246, L284 C:B944, G:B831, U:B568 A:B945, A:B2448 2z4n B2908 3Pout·2Bout B3028, B3029, B3030, B3031, B3032, L145 U:B568, G:B831, C:B944 A:B945, A:B2448 2z4n B2910 3Pout·2Bout B3037, B3038, B3039, B3040, B3041, B3042 A:B1936, G:B1959, A:B1937 A:B1960, G:B1959 3df2 B3157 3Pout·2Bout B4158, B4159, B4160, B4161, B4162, B4163 A:B1937, A:B1936, G:B1959 A:B1960, G:B1959 3df2 B3282 3Pout·2Bout B4283, B4284, B4285, B4286, B4287, B4288 C:B944, G:B831, U:B568 A:B945, A:B2448 3df4 B3014 3Pout·2Bout B4015, B4016, B4017, B4019, B4020, L4018 U:B568, G:B831, C:B944 A:B945, A:B2448 3i1p A2968 3Pout·2Bout A3340, A3341, A3342, A3343, A3344, A3345 A:A2051, G:A2578, C:A2050 A:A2051, A:A2614 3i1t A2953 3Pout·2Bout A3267, A3268, A3269, A3270, A3271 G:A1456, A:A1453, C:A1454 G:A1456, U:A1457

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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