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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2i2v:B2921, See in JSmolMgRNA representative site for type 2NB Click on the image to toggle views


Site type: 2Nb

Schematic drawing for
2Nb
MgRNA type 2NB
List of all 158 Mg2+ binding sites with the site type 2Nb 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 7 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2i2t B2932 2Nb G:B1358(N7), G:B1371(N7) B3156, B3157, B3158, B3159 G:B1358, C:B1357, C:B1370
2i2t B2959 2Nb G:B733(N7), A:B761(N7) B3284, B3285, B3286, B3287 A:B761, G:B733, G:B760, C:B732
2i2u A1560 2Nb G:A858(N7), G:A869(N7) A1682, A1683, A1684, A1685 G:A869, G:A858, C:A868, C:A857
2i2v B2921 2Nb G:B733(N7), A:B761(N7) B3106, B3107, B3108, B3109 G:B733, G:B760, A:B761, C:B732
2i2v B2941 2Nb G:B1358(N7), G:B1371(N7) B3205, B3206, B3207, B3208 G:B1371, G:B1358, C:B1357, C:B1370
2otj 08011 2Nb G:0824(N7), G:0854(N7) 03987, 04323, 04452, 04558 G:0854, G:0824, U:0823, C:0853
2qal A2187 2Nb G:A858(N7), G:A869(N7) A2188, A2189, A2190, A2191 G:A858, G:A869, C:A868
2qam B3321 2Nb G:B733(N7), A:B761(N7) B3873, B3874, B3875, B3876 A:B761, G:B760, G:B733
2qao B3099 2Nb G:B733(N7), A:B761(N7) B3699, B3700, B3701, B3702 A:B761, G:B760, G:B733
2qao B3220 2Nb G:B1358(N7), G:B1371(N7) B3800, B3801, B3802, B3803 G:B1371, G:B1358, C:B1357, C:B1370
2qb9 A2187 2Nb G:A858(N7), G:A869(N7) A2509, A2510, A2511, A2512 G:A858, G:A869, C:A868
2qba B3321 2Nb G:B733(N7), A:B761(N7) B3873, B3874, B3875, B3876 A:B761, G:B760, C:B732, G:B733
2qba B3164 2Nb G:B1358(N7), G:B1371(N7) B3745, B3746, B3747, B3748 G:B1358, G:B1371, C:B1357
2qbb A2213 2Nb G:A858(N7), G:A869(N7) A2545, A2546, A2547, A2548 G:A869, G:A858, C:A868, C:A857
2qbc B3099 2Nb G:B733(N7), A:B761(N7) B3701, B3702, B3703, B3704 A:B761, G:B733, G:B760, C:B732
2qbd A2187 2Nb G:A858(N7), G:A869(N7) A2188, A2189, A2190, A2191 G:A858, G:A869, C:A868
2qbe B3321 2Nb G:B733(N7), A:B761(N7) B3873, B3874, B3875, B3876 A:B761, G:B760, C:B732, G:B733
2qbf A1576 2Nb G:A858(N7), G:A869(N7) A1777, A1778, A1779, A1780 G:A869, G:A858, C:A868, C:A857
2qbg B2941 2Nb G:B1358(N7), G:B1371(N7) B3199, B3200, B3201, B3202 G:B1371, G:B1358, C:B1357, C:B1370
2qbg B2921 2Nb G:B733(N7), A:B761(N7) B3098, B3099, B3100, B3101 A:B761, G:B733, G:B760, C:B732
2qbh A1573 2Nb G:A858(N7), G:A869(N7) A1750, A1751, A1752, A1753 G:A858, G:A869, C:A868
2qbi B2932 2Nb G:B1358(N7), G:B1371(N7) B3147, B3148, B3149, B3150 G:B1358, G:B1371, C:B1357, C:B1370
2qbi B2959 2Nb G:B733(N7), A:B761(N7) B3273, B3274, B3275, B3276 A:B761, G:B733, G:B760, C:B732
2qbj A1576 2Nb G:A858(N7), G:A869(N7) A1775, A1776, A1777, A1778 G:A869, G:A858, C:A868, C:A857
2qbk B2941 2Nb G:B1358(N7), G:B1371(N7) B3195, B3196, B3197, B3198 G:B1371, G:B1358, C:B1357, C:B1370

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>