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

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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1jj2 08011 2Nb G:0824(N7), G:0854(N7) 03487, 03819, 03956, 04061 G:0854, G:0824, U:0823, C:0853
1m90 A8011 2Nb G:A824(N7), G:A854(N7) A3486, A3824, A3961, A4065 G:A854, U:A823, G:A824, C:A853
1q81 A8011 2Nb G:A824(N7), G:A854(N7) A3472, A3795, A3926, A4033 G:A854, G:A824, U:A823, C:A853
1s72 08011 2Nb G:0824(N7), G:0854(N7) 03481, 03815, 03951, 04055 G:0854, G:0824, U:0823, C:0853
1vq4 08011 2Nb G:0824(N7), G:0854(N7) 04265, 04597, 04724, 04824 G:0854, U:0823, G:0824, C:0853
1vq5 08011 2Nb G:0824(N7), G:0854(N7) 04272, 04604, 04736, 04836 G:0854, U:0823, G:0824, C:0853
1vq6 08011 2Nb G:0824(N7), G:0854(N7) 04265, 04594, 04722, 04822 G:0854, U:0823, G:0824, C:0853
1vq7 08011 2Nb G:0824(N7), G:0854(N7) 04283, 04616, 04746, 04847 G:0854, U:0823, G:0824, C:0853
1vs5 A1574 2Nb G:A858(N7), G:A869(N7) A1752, A1753, A1754, A1755 G:A858, G:A869, C:A868
1vs6 B2959 2Nb G:B733(N7), A:B761(N7) B3276, B3277, B3278, B3279 G:B733, G:B760, A:B761, C:B732
1vs7 A1578 2Nb G:A858(N7), G:A869(N7) A1777, A1778, A1779, A1780 G:A869, G:A858, C:A868
1vs8 B2921 2Nb G:B733(N7), A:B761(N7) B3096, B3097, B3098, B3099 A:B761, G:B733, G:B760, C:B732
1vs8 B2940 2Nb G:B1358(N7), G:B1371(N7) B3191, B3192, B3193, B3194 G:B1371, G:B1358, C:B1357, C:B1370
1vt2 A2950 2Nb G:A1358(N7), G:A1371(N7) A3255, A3256, A3257, A3258 G:A1358, C:A1357, G:A1371
1vt2 A2924 2Nb G:A733(N7), A:A761(N7) A3142, A3143, A3144, A3145 A:A761, G:A733, G:A760, C:A732
1w2b 03924 2Nb G:0824(N7), G:0854(N7) 05060, 05157, 05158, 05159 U:0823, G:0824, C:0853, G:0854
1yij 08011 2Nb G:0824(N7), G:0854(N7) 03970, 04307, 04439, 04544 G:0854, G:0824, U:0823, C:0853
1yj9 08011 2Nb G:0824(N7), G:0854(N7) 03776, 04115, 04247, 04355 G:0854, G:0824, U:0823, C:0853
1yjw 78011 2Nb G:0824(N7), G:0854(N7) 05841, 05842, 05941, 05943 U:0823, G:0824, G:0854
2avy A1572 2Nb G:A858(N7), G:A869(N7) A1746, A1747, A1748, A1749 G:A858, G:A869, C:A868
2aw4 B2932 2Nb G:B1358(N7), G:B1371(N7) B3146, B3147, B3148, B3149 G:B1358, G:B1371, C:B1357, C:B1370
2aw4 B2959 2Nb G:B733(N7), A:B761(N7) B3272, B3273, B3274, B3275 A:B761, G:B733, G:B760, C:B732
2aw7 A1577 2Nb G:A858(N7), G:A869(N7) A1779, A1780, A1781, A1782 G:A869, G:A858, C:A868, C:A857
2awb B2941 2Nb G:B1358(N7), G:B1371(N7) B3195, B3196, B3197, B3198 G:B1371, G:B1358, C:B1357, C:B1370
2i2p A1573 2Nb G:A858(N7), G:A869(N7) A1755, A1756, A1757, A1758 G:A858, G:A869, C:A868 C:A857

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>