MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

Back to Classification Home Download this subset in: CSV, XML, JSON
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

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 1 of 12 | « Previous | | 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
1jj2 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03148, 07337, 08526, 08544 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1jj2 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03149, 07391, 07392, 08760 A:0882, C:0884 U:0883, A:01836
1k73 A8077 trans-2Oph C:A880(OP1), U:A883(OP2) A3617, A7855, A7856, A9239 A:A882, C:A884 U:A883, A:A1836
1k8a A8077 trans-2Oph C:A880(OP1), U:A883(OP2) A3213, A7393, A7394, A8835 A:A882, C:A884 U:A883, A:A1836
1k8a A8015 trans-2Oph A:A844(OP1), A:A1689(OP1) A3211, A7338, A8607, A8625 G:A1688 A:A844, A:A1689, C:A1690, A:A882, C:A1692
1k9m A8077 trans-2Oph C:A880(OP1), U:A883(OP2) A3614, A7854, A7855, A9239 A:A882, C:A884 U:A883, A:A1836
1kqs 08052 trans-2Oph U:01125(OP1), G:93092(OP1) 03132, 07372, 09103, 92357 C:01126 C:01129, G:93090
1kqs 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03131, 07326, 07327, 08758 A:0882, C:0884 U:0883, A:01836
1m90 A8015 trans-2Oph A:A844(OP1), A:A1689(OP1) A3150, A7320, A8526, A8544 G:A1688 A:A844, A:A1689, C:A1690, A:A882, C:A1692
1m90 A8077 trans-2Oph C:A880(OP1), U:A883(OP2) A3151, A7374, A7375, A8762 A:A882, C:A884 U:A883, A:A1836
1nji A8077 trans-2Oph C:A880(OP1), U:A883(OP2) A3616, A7836, A7837, A9238 A:A882, C:A884 U:A883, A:A1836
1q81 A8077 trans-2Oph C:A880(OP1), U:A883(OP2) A3135, A7325, A7326, A8758 A:A882, C:A884 U:A883, A:A1836
1q81 A8015 trans-2Oph A:A844(OP1), A:A1689(OP1) A3133, A7270, A8526, A8545 G:A1688 A:A844, A:A1689, C:A1690, A:A882, C:A1692
1q86 A8077 trans-2Oph C:A880(OP1), U:A883(OP2) A3148, A7346, A7347, A8765 A:A882, C:A884 U:A883, A:A1836
1qvf 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03140, 07239, 08543 A:0844, A:01689, C:01692
1qvf 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03141, 07292, 07293, 08764 A:0882, C:0884 U:0883, A:01836
1qvg 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03127, 07224, 07225, 08765 A:0882, C:0884 U:0883, A:01836
1s72 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03143, 07292, 08526, 08544 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1s72 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03144, 07346, 07347, 08760 A:0882, C:0884 U:0883, A:01836
1vq4 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03927, 08105, 08109, 09559 A:0882, C:0884 U:0883, A:01836
1vq4 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03925, 07956, 09326, 09344 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
1vq5 98052 trans-2Oph U:01125(OP1), G:93092(OP1) 03939, 08207, 9737, 92357 C:01126 C:01129, G:93090
1vq5 08015 trans-2Oph A:0844(OP1), A:01689(OP1) 03937, 08052, 09345, 19203 G:01688 A:0844, A:01689, C:01690, C:01692, A:0882
1vq5 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03938, 08161, 08162, 09564 A:0882, C:0884 U:0883, A:01836
1vq6 08077 trans-2Oph C:0880(OP1), U:0883(OP2) 03930, 08125, 08126, 09566 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
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>