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

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Representative site 1vs8:B2991, See in JSmolMgRNA representative site for type trans,cis-4OP  Click on the image to toggle views


Site type: trans,cis-4Oph

Schematic drawing for
trans,cis-4Oph

MgRNA type trans,cis-4OP
List of all 29 Mg2+ binding sites with the site type trans,cis-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
1l8v B305 trans,cis-4Oph A:B184(OP1), A:B186(OP1), A:B187(OP2), G:B188(OP2)
1vs6 B2991 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3419, B3420 U:B827
1vs8 B2991 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3426, B3427 U:B827
1vvu A3054 trans,cis-4Oph G:A1271(OP2), A:A1272(OP2), G:A1647(OP1), C:A1648(OP1)
1vx9 A3055 trans,cis-4Oph G:A1271(OP2), A:A1272(OP2), G:A1647(OP1), C:A1648(OP1)
2aw4 B2991 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3415, B3416 U:B827
2awb B2992 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3427, B3428 U:B827
2i2t B2991 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3425, B3426 U:B827
2qam B3496 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B4016, B4017 U:B827
2qao B3512 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B4035, B4036 U:B827
2qba B3496 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B4013, B4014 U:B827
2qbe B3496 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B4013, B4014 U:B2259, U:B827
2qbg B2993 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3434, B3435 U:B827
2qbi B2991 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3415, B3416 U:B827
2qov B2991 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3419, B3420 U:B827
2qox B2955 trans,cis-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3259, B3260
2qoz B2991 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3909, B3910 U:B827
3df2 B3496 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B4497, B4498 U:B827
3df4 B3512 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B4513, B4514 U:B827
3i1p A2946 trans,cis-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3237, A3238
3ofr A3012 trans,cis-4Oph U:A826(OP1), C:A2427(OP2), G:A2428(OP1), G:A2429(OP1) A3537, A3538 U:A827
3r8t A3012 trans,cis-4Oph U:A826(OP1), C:A2427(OP1), G:A2428(OP1), G:A2429(OP1) A3572, A3573 U:A2259, U:A827
4bye A3940 trans,cis-4Oph U:A826(OP1), C:A2427(OP1), G:A2428(OP1), G:A2429(OP1)
4gar A3039 trans,cis-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3389, A3390 G:A1271
4kix A3107 trans,cis-4Oph U:A826(OP1), C:A2427(OP1), G:A2428(OP1), G:A2429(OP1) A3691 U:A827

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>