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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 4 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
1vq4 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 04050, 07949, 07950
1vq4 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03971, 09341, A9330
1vq4 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03919, 07946, 09496 U:02484 G:02482, A:02532
1vq5 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03982, 09342, A9328
1vq5 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 08069, 08073, 09718 C:02542
1vq5 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03931, 07991, 09500 U:02484 A:02532, G:02482
1vq5 08006 fac-3Oph U:0821(OP2), C:0822(OP2), G:0854(OP1) 03130, 03933, 04068 U:0855, G:0856
1vq5 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 04060, 07994, 07995
1vq6 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 04054, 07958, 07959
1vq6 08006 fac-3Oph U:0821(OP2), C:0822(OP2), G:0854(OP1) 03121, 03924, 04062 U:0855, G:0856
1vq6 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07970, 07971, 09714 C:02542
1vq6 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03974, 09342, A9330
1vq6 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03922, 07955, 09501 U:02484 A:02532, G:02482
1vq7 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 08000, 08052, 09719 C:02542
1vq7 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03939, 07986, 09504 U:02484 G:02482, A:02532
1vq7 08006 fac-3Oph U:0821(OP2), C:0822(OP2), G:0854(OP1) 03131, 03941, 04078 U:0855, G:0856
1vq7 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 04069, 07989, 07990
1vq7 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03990, 09341, A9332
1vq8 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 03016, 08319, 08320 C:02542
1vq8 08029 fac-3Oph U:01503(OP1), A:01504(OP2), C:01679(OP1) 03817, 08325, 08327
1vq8 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 04209, 08304, 09800 U:02484 A:02532, G:02482
1vq8 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04259, 09648, A9522
1vq9 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04230, A9540, A9567
1vq9 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 08216, 08217, 08218 C:02542
1vqk 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04270, A9499, A9520

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>