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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 1vs6:B3008, See in JSmolMgRNA representative site for type cis-2OP-NB Click on the image to toggle views


Site type: cis-2Oph·Nb

Schematic drawing for
cis-2Oph·Nb
MgRNA type cis-2OP-NB
List of all 118 Mg2+ binding sites with the site type cis-2Oph·Nb 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 4 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
3i1n A3029 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3607, A3608, A3609 G:A194, A:A195 G:A194
3i1p A3024 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3577, A3578, A3579 G:A194, A:A195 G:A194
3i1r A3028 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3606, A3607, A3608 G:A194, A:A195 G:A194
3i1t A3024 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3580, A3581, A3582 G:A194, A:A195
3i20 A3028 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3606, A3607, A3608 G:A194, A:A195
3i22 A3023 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3581, A3582, A3583 G:A194, A:A195 G:A194
3i56 08061 cis-2Oph·Nb A:0167(OP1), C:0168(OP2) A:0165(N7) 08331, 08337, 08350 G:0164, A:0165 G:0164
3oas A3023 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3579, A3580, A3581 G:A194 G:A194
3ofc A3027 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3599, A3600, A3601 G:A194
3ofd A3023 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3580, A3581, A3582 G:A194
3ofq A3024 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3580, A3581, A3582 G:A194
3ofr A3028 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3596, A3597, A3598 G:A194 G:A194
3ofz A3026 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3588, A3589, A3590 G:A194, A:A195 G:A194
3og0 A3022 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3579, A3580, A3581 G:A194
3orb A3027 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3602, A3603, A3604 G:A194
3orb A3030 cis-2Oph·Nb C:A510(OP1), U:A511(OP2) G:A512(N7) A3613, A3614, A3615
3r8s A3029 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3666, A3667, A3668 G:A194, A:A195 G:A194
3r8s A3032 cis-2Oph·Nb C:A510(OP1), U:A511(OP2) G:A512(N7) A3677, A3678, A3679
3v23 A3540 cis-2Oph·Nb C:A510(OP1), U:A511(OP2) G:A512(N7) A4760, A4761, A4762 C:A509
3v2d A3137 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A4064, A4065 G:A194, A:A195
3v2f A3189 cis-2Oph·Nb C:A510(OP1), U:A511(OP2) G:A512(N7) A3884, A3885, A3886 C:A509
4kix A3123 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3748 G:A194
4kj1 A3127 cis-2Oph·Nb C:A510(OP1), U:A511(OP2) G:A512(N7) A3762, A3763
4kj7 A3127 cis-2Oph·Nb C:A510(OP1), U:A511(OP2) G:A512(N7) A3759, A3760, A3761
4kj9 A3126 cis-2Oph·Nb C:A510(OP1), U:A511(OP2) G:A512(N7) A3766

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>