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

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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 2 of 16 | | | 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
1kqs 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03174, 08543, A8537
1kqs 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07278, 07279, 08903 C:02542
1kqs 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 03256, 07265, 07266
1m1k A8006 fac-3Oph U:A821(OP2), C:A822(OP2), G:A854(OP1) A3213, A3349, A9409 G:A856, U:A855
1m1k A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3211, A7366, A8771 U:A2484 A:A2532, G:A2482
1m1k A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3260, C8512, C8537
1m1k A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3342, A7369, A7370
1m90 A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3144, A7309, A8697 U:A2484 A:A2532, G:A2482
1m90 A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3275, A7312, A7313
1m90 A8026 fac-3Oph C:A2608(OP1), G:A2609(OP1), U:A2610(OP2) A7326, A7327, A8913 C:A2542
1m90 A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3194, A8541, C8536
1m90 A8006 fac-3Oph U:A821(OP2), C:A822(OP2), G:A854(OP1) A3146, A3282, A9330 G:A856, U:A855
1n8r A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A4142, A8265, A8266
1n8r A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A4011, A8262, A9577 U:A2484 A:A2532
1nji A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3738, A7772, A7773
1nji A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3659, A9820, C8511
1nji A8026 fac-3Oph C:A2608(OP1), G:A2609(OP1), U:A2610(OP2) A7786, A7787, A9387 C:A2542
1q7y A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3255, A7256
1q7y A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3126, A7252, A8693 U:A2484 A:A2532, G:A2482 G:A2482
1q7y A8006 fac-3Oph U:A821(OP2), C:A822(OP2), G:A854(OP1) A3128, A3263, A9326 U:A855, G:A856
1q7y A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3174, A8542, A9341
1q81 A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3179, A8542, C8539
1q81 A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3127, A7260, A8699 U:A2484 A:A2532, G:A2482
1q81 A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3259, A7263, A7264
1q81 A8006 fac-3Oph U:A821(OP2), C:A822(OP2), G:A854(OP1) A3129, A3267, A9326 G:A856, U:A855

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>