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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qbg:B2955, See in JSmolMgRNA representative site for type trans,trans-4OPClick on the image to toggle views


Site type: trans,trans-4Oph

Schematic drawing for
trans,trans-4Oph
MgRNA type trans,trans-4OP
List of all 35 Mg2+ binding sites with the site type trans,trans-4Oph 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3i1t A2946 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3239, A3240
3i20 A2944 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3229, A3230
3iin B1 trans,trans-4Oph C:B88(OP1), G:B170(OP1), A:B172(OP1), DA:C207(OP2) DT:D3(O3')
3oat A2943 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3220, A3221
3ofr A2944 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3225, A3226
3r8s A2944 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3284, A3285
3r8t A2943 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3257, A3258
4kix A3040 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3380, A3381
4kiz A3040 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3379
4qd1 A3255 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), G:A1647(OP1), C:A1648(OP1)

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>