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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 5 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
3ofo A1557 2Nb G:A858(N7), G:A869(N7) A1695, A1696, A1697, A1698 G:A858, G:A869, C:A868
3ofp A1559 2Nb G:A858(N7), G:A869(N7) A1694, A1695, A1696, A1697 G:A858, G:A869, C:A868
3ofq A2925 2Nb G:A733(N7), A:A761(N7) A3140, A3141, A3142, A3143 A:A761, G:A733, G:A760, C:A732 G:A760
3ofq A2950 2Nb G:A1358(N7), G:A1371(N7) A3255, A3256, A3257, A3258 G:A1358, C:A1357, G:A1371
3ofr A2923 2Nb G:A733(N7), A:A761(N7) A3130, A3131, A3132, A3133 A:A761, G:A733, G:A760 C:A732
3ofr A2948 2Nb G:A1358(N7), G:A1371(N7) A3243, A3244, A3245, A3246 G:A1371
3ofx A1558 2Nb G:A858(N7), G:A869(N7) A1698, A1699, A1700, A1701 G:A858, G:A869, C:A857, C:A868
3ofy A1559 2Nb G:A858(N7), G:A869(N7) A1697, A1698, A1699, A1700 G:A858, G:A869, C:A868
3ofz A2946 2Nb G:A1358(N7), G:A1371(N7) A3236, A3237, A3238, A3239 G:A1358, G:A1371, C:A1357
3og0 A2948 2Nb G:A1358(N7), G:A1371(N7) A3252, A3253, A3254, A3255 G:A1358, C:A1357, G:A1371
3og0 A2923 2Nb G:A733(N7), A:A761(N7) A3139, A3140, A3141, A3142 A:A761, G:A733, G:A760, C:A732
3or9 A1559 2Nb G:A858(N7), G:A869(N7) A1699, A1700, A1701, A1702 G:A858, G:A869, C:A868
3r8t A2947 2Nb G:A1358(N7), G:A1371(N7) A3275, A3276, A3277, A3278 G:A1371, G:A1358, C:A1357
3v23 A3302 2Nb G:A733(N7), A:A761(N7) A3894, A3895, A3896, A3897 C:A732, G:A733, G:A760, A:A761
3v27 A3312 2Nb G:A733(N7), A:A761(N7) A3869, A3870, A3871, A3872 C:A732, G:A733, G:A760, A:A761
3v29 A3343 2Nb G:A733(N7), A:A761(N7) A3788, A3789, A3790, A3791 A:A761, G:A733, C:A732
3v2d A3130 2Nb G:A733(N7), A:A761(N7) A4046, A4047, A4048, A4049 C:A732, G:A733, G:A760, A:A761
3v2f A3166 2Nb G:A733(N7), A:A761(N7) A3810, A3811, A3812, A3813 G:A760, A:A761, G:A733, C:A732
4dha A3815 2Nb G:A733(N7), A:A761(N7) A5142, A5143, A5144 C:A732, A:A761
4dhc A3384 2Nb G:A733(N7), A:A761(N7) A3815, A3816, A3817, A3818 G:A760, A:A761, G:A733 C:A732
4gaq A1625 2Nb G:A858(N7), G:A869(N7) A1817, A1818, A1819, A1820 G:A858, G:A869, C:A857
4kj0 A1625 2Nb G:A858(N7), G:A869(N7) A1810, A1811 G:A858, C:A868, G:A869
4kj8 A1625 2Nb G:A858(N7), G:A869(N7) A1813, A1814, A1816 G:A858, C:A868, G:A869
4kja A1624 2Nb G:A858(N7), G:A869(N7) A1817, A1819 G:A869
4nvv A3316 2Nb G:A780(N7), A:A808(N7) A4100, A4101, A4102, A4103 C:A779, G:A780, G:A807, A:A808

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>