MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1egk:C14, See in JSmolClick on the image to toggle views Site type: Bout Schematic drawing for Bout List of all 132 Mg2+ binding sites with the site type 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 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 2qp0 A1593 Bout A2128, A2129, A2130, A2131, A2132, A2133 G:A941 2z4l B2948 Bout B3212, B3213, B3214, B3215, B3216, B3217 U:B434 3df3 A2312 Bout A4313, A4314, A4315, A4316, A4317, A4318 G:A38 3df3 A2107 Bout A4109, A4112, A4113, E4108, E4110, E4111 G:A1077 3df4 B3389 Bout B4390, B4391, B4392, B4393, B4394, B4395 G:B651 3i1t A2919 Bout A3117, A3118, A3119, A3120, A3121, A3122 U:A580 3i1t A2923 Bout A3138, A3139, A3140, A3141, A3142, A3143 G:A651 3i22 A3033 Bout A3624, A3625, A3626, 4758, 4760, 4763 G:A2742 3oat A2918 Bout A3109, A3110, A3111, A3112, A3113, A3114 A:A1260 3ofp A1536 Bout A1584, A1585, A1586, A1587, A1588 G:A362 3ofq A2924 Bout A3134, A3135, A3136, A3137, A3138, A3139 G:A651 3ofx A1569 Bout A1746, A1747, A1748, A1749, A1750, U219 G:A1525 3r1l F1031 Bout F1052, F1053, F1054, F1055, F1056, F1057 G:F105 3r8t A2994 Bout A3493, A3494, A3495, A3496, A3497, A3498 G:A1410 3td0 B5000 Bout A5001, A5006, B5002, B5003, B5004, B5005 A:B40 3v23 0102 Bout A4019, A4020, 0203, 0204, 0205, 0206 G:A2280 3v23 A3601 Bout A5000, A5001, A5002, A5003, A5004, A5005 G:A2000 3v23 A3596 Bout A4970, A4971, A4972, A4973, A4974, A4975 G:A463 3v25 A3421 Bout A4158, A4159, A4160, A4161 G:A2819 3v25 A3422 Bout A4162, A4163, A4164, A4165, A4166, A4167 G:A1907 3v25 A3427 Bout A4187, A4188, A4189, A4190 G:A2000 3v26 A1699 Bout A1895, A1896, A1897, A1898, A1899, A1900 C:A48 3v27 A3366 Bout A4095, A4096, A4097, 0203, 0204, 0205 G:A2280 3v27 A3622 Bout A5189, A5190, A5191, A5192, A5193, A5194 G:A2000 3v27 A3648 Bout A5325, A5326, A5327, A5328, A5329, A5330 G:A696

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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