`

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

Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 1yhq:08001, See in JSmolMgRNA representative site for type fac-3OP        Click on the image to toggle views


Site type: fac-3Oph

Schematic drawing for
fac-3Oph

MgRNA type fac-3OP
List of all 392 Mg2+ binding sites with the site type fac-3Oph 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 16 | « 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
1ffk 02925 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 02927, 02928, 02929 U:02484 G:02482, A:02532
1hr2 B2 fac-3Oph A:B183(OP1), A:B184(OP2), A:B186(OP2) B326, B327, B328 A:B184, A:B186
1hr2 A1 fac-3Oph A:A183(OP1), A:A184(OP2), A:A186(OP2) A322, A323, A324 A:A184, A:A186
1j1u B1501 fac-3Oph A:B509(OP1), G:B510(OP2), U:B548(OP1) B60, B350 U:B511
1jj2 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 03273, 07330, 07331
1jj2 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03142, 07327, 08694 U:02484 A:02532, G:02482
1jj2 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03193, A8512, A8535
1jj2 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07343, 07344, 08912 C:02542
1k73 A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3611, A7791, A9176 U:A2484 A:A2532, G:A2482 G:A2482
1k73 A8006 fac-3Oph U:A821(OP2), C:A822(OP2), G:A854(OP1) A3613, A3748, A9808 G:A856, U:A855
1k73 A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3661, C8511, C8534
1k73 A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3741, A7794, A7795
1k8a A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3332, A7331, A7332
1k8a A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3206, A7328, A8772 U:A2484 G:A2482, A:A2532
1k9m A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3657, A9021, C8537
1k9m A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3736, A7791, A7792
1k9m A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3608, A7788, A9178 U:A2484 G:A2482, A:A2532
1kc8 A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3671, A9024, C8536
1kc8 A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3619, A7777, A9178 U:A2484 G:A2482, A:A2532
1kc8 A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3751, A7780, A7781
1kd1 A8006 fac-3Oph U:A821(OP2), C:A822(OP2), G:A854(OP1) A3613, A3750, A9805 G:A856, U:A855
1kd1 A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3742, A7777, A7778
1kd1 A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3662, C8511, C8536
1kd1 A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3611, A7774, A9173 U:A2484 A:A2532
1kqs 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03123, 07262, 08694 U:02484 A:02532, G:02482

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>