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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 2 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
1vq6 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03930, 08125, 08126, 09566 A:0882, C:0884 U:0883, A:01836
1vq7 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03946, 08156, 08157, 09568 A:0882, C:0884 U:0883, A:01836
1vq7 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03945, 07995, 09326, 09344 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1vq7 98052 trans-2Oph U:01125(OP1), G:93092(OP1) 03947, 08203, 9737, 92357 C:01126 C:01129, G:93090
1vq8 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04214, 08315, 09633, 09651 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1vq9 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04184, 08212, 09649, 19461 G:01688 A:0844, A:0882, A:01689, C:01690, C:01692
1vqk 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04225, 08353, 09633, 09650 G:01688 A:0844, A:01689, A:0882, C:01692
1vql 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04214, 08318, 09633, 09650 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1vqm 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04222, 08320, 09633, 09650 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1vqn 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04217, 08311, 09633, 09650 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1vqo 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04237, 08366, 09633, 09649 G:01688 A:0844, A:01689, A:0882, C:01692
1vqp 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 04233, 08338, 09633, 09650 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1vs6 B2960 trans-2Oph A:B751(OP1), A:B1614(OP1) B3280, B3281, B3282, B3283 G:B1613 A:B751, C:B1617, A:B1614, A:B789
1vs6 B3007 trans-2Oph C:B787(OP1), U:B790(OP2) B3484, B3485, B3486, B3487
1vs8 B2919 trans-2Oph U:B999(OP2), C:B1153(OP2) B3086, B3087, B3088, B3089 C:B998 C:B1152 G:B1154
1vs8 B2959 trans-2Oph A:B751(OP1), A:B1614(OP1) B3279, B3280, B3281, B3282 G:B1613 A:B1614, C:B1615, C:B1617, A:B789
1vs8 B3005 trans-2Oph C:B787(OP1), U:B790(OP2) B3477, B3478, B3479, B3480 C:B791
1vt2 A2940 trans-2Oph U:A999(OP2), C:A1153(OP2) A3210, A3211, A3212, A3213 C:A998, C:A1152 G:A1154
1vt2 A2927 trans-2Oph A:A751(OP1), A:A1614(OP1) A3156, A3157, A3158, A3159 G:A1613 A:A751, A:A789
1w2b 03928 trans-2Oph A:0844(OP1), A:01689(OP1) 05233, 05239, 06754, 06761 G:01688 A:0844, A:0882, A:01689, C:01690, C:01692
1yhq 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 04117, 08303, 09504, 09522 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1yi2 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03619, 07748, 09004, 09022 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1yi2 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03620, 07801, 07802, 09240 A:0882, C:0884 U:0883, A:01836
1yij 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03631, 07760, 09004, 09023 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1yij 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03632, 07814, 07815, 09241 A:0882, C:0884 U:0883, A:01836

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>