`

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

Back to Classification Home Download this subset in: CSV, XML, JSON
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"
Page 1 of 2 | « Previous | | 1 | 2
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1vs6 B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3205, B3206
1vs8 B2954 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3255, B3256
1vvm A3054 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), G:A1647(OP1), C:A1648(OP1)
1x8w B2 trans,trans-4Oph A:B184(OP1), A:B186(OP1), A:B187(OP2), G:B188(OP2)
2aw4 B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3201, B3202
2awb B2955 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3259, B3260
2i2t B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3211, B3212
2i2v B2955 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3268, B3269
2qam B3232 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3799, B3800
2qao B3298 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3863, B3864
2qba B3232 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3801, B3802
2qbc B3298 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3863, B3864
2qbe B3232 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3800, B3801
2qbg B2955 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3262, B3263
2qbi B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3201, B3202
2qbk B2955 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3258, B3259
2qoz B2944 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3695, B3696
2qp1 B2955 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3765, B3766
2r8s R1002 trans,trans-4Oph A:R184(OP1), A:R186(OP1), A:R187(OP2), G:R188(OP2) R1008, R1009 A:R183
2z4l B2945 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3201, B3202
2z4n B2956 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3261, B3262
3df2 B3232 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B4233, B4234
3df4 B3298 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B4299, B4300
3i1n A2944 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3231, A3232
3i1r A2944 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3228, A3229

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>