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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qan:A2288, See in JSmolMgRNA representative site for type 4BO Click on the image to toggle views


Site type: 4Bout

Schematic drawing for
4Bout
MgRNA type 4BO
List of all 105 Mg2+ binding sites with the site type 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 2 of 5 | | | 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
3i1z A1543 4Bout A1621, A1622, A1623, A1624, A1625, A1626 G:A646, G:A592, U:A593, G:A645
3ivk C122 4Bout C138, C139, C140, C141, C142, C143 A:C97, G:C91, G:C92, U:C93
3oas A2971 4Bout A3360, A3361, A3362, A3363, A3364, A3365 G:A2242, U:A2243, A:A2241, U:A2074
3oat A2992 4Bout A3447, A3448, A3449, A3450, A3451, A3452 G:A1410, U:A1411, U:A1409, A:A1590
3oat A3033 4Bout A3618, A3619, C752, C753, C755 G:A2592, U:A2593, C:A2594, G:A2599
3ofa A1543 4Bout A1620, A1621, A1622, A1623, A1624, A1625 G:A646, G:A592, U:A593, G:A645
3ofc A2918 4Bout A3110, A3111, A3112, A3113, A3114, A3115 G:A1259, A:A1260, U:A580, U:A1258
3ofo A1543 4Bout A1619, A1620, A1621, A1622, A1623, A1624 G:A646, G:A592, U:A593, G:A645
3ofq A2972 4Bout A3361, A3362, A3363, A3364, A3365, A3366 G:A2238, G:A2242, A:A2241, U:A2243
3ofq A2926 4Bout A3144, A3145, A3146, A3147, A3148, A3149 U:A755, G:A757, A:A739, A:A756
3ofr A2919 4Bout A3111, A3112, A3113, A3114, A3115, A3116 G:A1259, A:A1260, U:A580, U:A1258
3ofz A2918 4Bout A3108, A3109, A3110, A3111, A3112, A3113 G:A1259, A:A1260, U:A580, U:A1258
3og0 A2970 4Bout A3358, A3359, A3360, A3361, A3362, A3363 G:A2242, U:A2243, A:A2241, U:A2074
3orb A2993 4Bout A3459, A3460, A3461, A3462, A3463, A3464 G:A1410, U:A1411, U:A1409, A:A1590
3r8s A2929 4Bout A3216, A3217, A3218, A3219, A3220, A3221 G:A797, C:A678, C:A679, G:A798
3r8s A2919 4Bout A3174, A3175, A3176, A3177, A3178, A3179 G:A1259, A:A1260, U:A580, U:A1258
3v23 A3577 4Bout A4877, A4878, A4879, A4880, A4881, A4882 U:A2457, G:A2494, G:A2495, G:A2455
3v23 A3594 4Bout A4958, A4959, A4960, A4961, A4962, A4963 G:A2843, G:A2844, G:A2845, C:A2871
3v27 A3359 4Bout A4064, A4065, A4066, A4067, A4068, A4069 G:A2843, G:A2844, G:A2845, C:A2871
3v27 A3430 4Bout A4349, A4350, A4351, A4352, A4353 G:A854, C:A923, G:A852, G:A853
3v27 A3437 4Bout A4382, A4383, A4384, A4385, A4386, A4387 U:A395, G:A379, U:A380, C:A378
3v27 A3562 4Bout A4927, A4928, A4929, A4930, A4931, A4932 G:A533, U:A534, G:A558, G:A559
3v27 A3628 4Bout A5224, A5225, A5226, A5227, A5228, A5229 U:A2457, G:A2494, G:A2495, G:A2455
3v27 B222 4Bout B347, B348, B349, B350, B351, B352 U:B80, U:B96, G:B97, G:B98
3v2d A3373 4Bout A4736, A4737, A4738, A4739, A4740 U:A2457, G:A2494, G:A2495, G:A2455

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].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>