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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3q3z:A6, See in JSmolMgRNA representative site for type trans-2OP Click on the image to toggle views


Site type: trans-2Oph

Schematic drawing for
trans-2Oph
MgRNA type trans-2OP
List of all 282 Mg2+ binding sites with the site type trans-2Oph 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 3 of 12 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1yj9 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03436, 07573, 08826, 08846 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1yjn 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03634, 07827, 07828, 09244 A:0882, C:0884 U:0883, A:01836
1yjw 78015 trans-2Oph A:0844(OP1), A:01689(OP1) 05913, 07606, 07619, 14004 G:01688 A:01689, C:01690, A:0844, C:01692, A:0882
1yjw 78077 trans-2Oph C:0880(OP1), U:0883(OP2) 06029, 06030, 06031, 06034 C:0884, A:0882 A:01836, U:0883
2aw4 B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3276, B3277, B3278, B3279 G:B1613 A:B751, C:B1617, A:B1614, A:B789
2awb B2919 trans-2Oph U:B999(OP2), C:B1153(OP2) B3087, B3088, B3089, B3090 C:B998 C:B1152 G:B1154
2awb B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3282, B3283, B3284, B3285 G:B1613 A:B1614, C:B1615, C:B1617, A:B789
2awb B3006 trans-2Oph C:B787(OP1), U:B790(OP2) B3478, B3479, B3480, B3481 C:B791
2i2t B3007 trans-2Oph C:B787(OP1), U:B790(OP2) B3488, B3489, B3490, B3491 A:B789, C:B791 A:B1780
2i2t B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3288, B3289, B3290, B3291 G:B1613 A:B751, A:B1614, C:B1617, C:B1615, A:B789
2i2v B3006 trans-2Oph C:B787(OP1), U:B790(OP2) B3485, B3486, B3487, B3488 C:B791 A:B1780
2i2v B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3292, B3293, B3294, B3295 G:B1613 A:B751, A:B789, C:B1617, A:B1614
2i2v B2919 trans-2Oph U:B999(OP2), C:B1153(OP2) B3096, B3097, B3098, B3099 C:B998 G:B1154
2otj 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03641, 07837, 07838, 09246 A:0882, C:0884 U:0883, A:01836
2otj 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03639, 07784, 09023, 18703 G:01688 A:0844, A:01689, C:01690, C:01692, A:0882
2otl 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03634, 07824, 07825, 09241 A:0882, C:0884 U:0883, A:01836
2otl 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03633, 07771, 09004, 09024 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
2qam B3326 trans-2Oph A:B751(OP1), A:B1614(OP1) B3877, B3878, B3879, B3880 G:B1613 A:B751, C:B1617, A:B1614, A:B789
2qao B3327 trans-2Oph A:B751(OP1), A:B1614(OP1) B3887, B3888, B3889, B3890 G:B1613 C:B1617, A:B1614, C:B1615, A:B789
2qao B3087 trans-2Oph U:B999(OP2), C:B1153(OP2) B3689, B3690, B3691, B3692 C:B998 G:B1154
2qao B3579 trans-2Oph C:B787(OP1), U:B790(OP2) B4087, B4088, B4089, B4090
2qba B3326 trans-2Oph A:B751(OP1), A:B1614(OP1) B3877, B3878, B3879, B3880 G:B1613 A:B751, C:B1617, A:B1614, C:B1615, A:B789
2qbc B3327 trans-2Oph A:B751(OP1), A:B1614(OP1) B3887, B3888, B3889, B3890 G:B1613 A:B751, C:B1617, A:B1614, C:B1615, A:B789
2qbc B3579 trans-2Oph C:B787(OP1), U:B790(OP2) B4087, B4088, B4089, B4090 C:B791 A:B1780
2qbc B3087 trans-2Oph U:B999(OP2), C:B1153(OP2) B3691, B3692, B3693, B3694 C:B998 C:B1152 G:B1154

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>