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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 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
1s72 08089 cis-2Oph·Nb A:0516(OP1), U:0517(OP2) G:0518(N7) 07353, 07404, 07405
1vq5 08079 cis-2Oph·Nb A:0167(OP1), C:0168(OP2) A:0165(N7) 03926, 03932, 03944 G:0164, A:0165 G:0164
1vs6 B3008 cis-2Oph·Nb A:B197(OP1), C:B198(OP2) A:B195(N7) B3488, B3489, B3490 G:B194, A:B195 G:B194
1vs6 B3011 cis-2Oph·Nb C:B510(OP1), U:B511(OP2) G:B512(N7) B3499, B3500, B3501 C:B509
1vs8 B3009 cis-2Oph·Nb C:B510(OP1), U:B511(OP2) G:B512(N7) B3492, B3493, B3494
1vs8 B3006 cis-2Oph·Nb A:B197(OP1), C:B198(OP2) A:B195(N7) B3481, B3482, B3483
1vt2 A3024 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3583, A3584, A3585 G:A194, A:A195 G:A194
1yi2 08079 cis-2Oph·Nb A:0167(OP1), C:0168(OP2) A:0165(N7) 03608, 03614, 03626 G:0164, A:0165 G:0164
1yi2 08089 cis-2Oph·Nb A:0516(OP1), U:0517(OP2) G:0518(N7) 07808, 07858, 07859 C:0515
1yij 08089 cis-2Oph·Nb A:0516(OP1), U:0517(OP2) G:0518(N7) 07821, 07870, 07871 C:0515
1yj9 08079 cis-2Oph·Nb A:0167(OP1), C:0168(OP2) A:0165(N7) 03425, 03431, 03443 G:0164, A:0165 G:0164
1yjn 08079 cis-2Oph·Nb A:0167(OP1), C:0168(OP2) A:0165(N7) 03621, 03627, 03640 G:0164, A:0165 G:0164
1yjw 78089 cis-2Oph·Nb A:0516(OP1), U:0517(OP2) G:0518(N7) 05225, 05229, 05231 C:0515
2aw4 B3011 cis-2Oph·Nb C:B510(OP1), U:B511(OP2) G:B512(N7) B3495, B3496, B3497
2aw4 B3008 cis-2Oph·Nb A:B197(OP1), C:B198(OP2) A:B195(N7) B3484, B3485, B3486 G:B194, A:B195 G:B194
2awb B3007 cis-2Oph·Nb A:B197(OP1), C:B198(OP2) A:B195(N7) B3482, B3483, B3484 G:B194
2awb B3010 cis-2Oph·Nb C:B510(OP1), U:B511(OP2) G:B512(N7) B3493, B3494, B3495
2i2t B3008 cis-2Oph·Nb A:B197(OP1), C:B198(OP2) A:B195(N7) B3492, B3493, B3494 A:B195 G:B194 G:B194
2i2v B3007 cis-2Oph·Nb A:B197(OP1), C:B198(OP2) A:B195(N7) B3489, B3490, B3491 G:B194, A:B195 G:B194
2i2v B3010 cis-2Oph·Nb C:B510(OP1), U:B511(OP2) G:B512(N7) B3500, B3501, B3502
2otl 08089 cis-2Oph·Nb A:0516(OP1), U:0517(OP2) G:0518(N7) 07831, 07880, 07881
2qam B3582 cis-2Oph·Nb A:B197(OP1), C:B198(OP2) A:B195(N7) B4084, B4085, B4086 G:B194, A:B195 G:B194
2qam B3596 cis-2Oph·Nb C:B510(OP1), U:B511(OP2) G:B512(N7) B4095, B4096, B4097
2qao B3598 cis-2Oph·Nb C:B510(OP1), U:B511(OP2) G:B512(N7) B4102, B4103, B4104
2qao B3584 cis-2Oph·Nb A:B197(OP1), C:B198(OP2) A:B195(N7) B4091, B4092, B4093 G:B194 G:B194

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>