Zinc in PDB 2y43: RAD18 Ubiquitin Ligase Ring Domain Structure

The structure of RAD18 Ubiquitin Ligase Ring Domain Structure, PDB code: 2y43 was solved by R.G.Hibbert, T.K.Sixma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.86 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.646, 29.357, 69.736, 90.00, 125.05, 90.00
R / Rfree (%)	17.505 / 22.311

The binding sites of Zinc atom in the RAD18 Ubiquitin Ligase Ring Domain Structure (pdb code 2y43). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the RAD18 Ubiquitin Ligase Ring Domain Structure, PDB code: 2y43:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the RAD18 Ubiquitin Ligase Ring Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RAD18 Ubiquitin Ligase Ring Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1097 b:15.6 occ:1.00 ND1 A:HIS43 2.1 14.5 1.0 SG A:CYS60 2.3 13.7 1.0 SG A:CYS41 2.3 12.6 1.0 SG A:CYS63 2.3 17.1 1.0 CE1 A:HIS43 3.0 19.0 1.0 CB A:CYS60 3.1 14.1 1.0 CB A:CYS41 3.1 14.9 1.0 CG A:HIS43 3.2 14.2 1.0 CB A:CYS63 3.4 19.4 1.0 CB A:HIS43 3.6 12.1 1.0 N A:CYS63 3.9 18.9 1.0 NE2 A:HIS43 4.1 18.1 1.0 CA A:CYS63 4.2 19.4 1.0 CD2 A:HIS43 4.2 16.4 1.0 CA A:CYS41 4.5 14.5 1.0 CG1 A:VAL65 4.5 15.4 1.0 N A:HIS43 4.5 11.7 1.0 CA A:CYS60 4.6 14.6 1.0 CB A:THR62 4.6 20.2 1.0 CA A:HIS43 4.7 10.9 1.0 O A:HOH2005 4.7 17.5 1.0 CD1 A:ILE38 4.7 13.6 1.0 C A:CYS41 4.7 13.8 1.0 O A:CYS41 4.8 13.7 1.0 C A:THR62 4.9 20.9 1.0 C A:CYS63 4.9 19.7 1.0

Zinc binding site 2 out of 4 in the RAD18 Ubiquitin Ligase Ring Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RAD18 Ubiquitin Ligase Ring Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1098 b:16.6 occ:1.00 SG A:CYS28 2.3 15.6 1.0 SG A:CYS25 2.3 14.1 1.0 SG A:CYS49 2.4 16.6 1.0 SG A:CYS46 2.4 16.0 1.0 CB A:CYS25 2.9 13.4 1.0 CB A:CYS46 3.2 14.0 1.0 CB A:CYS28 3.2 19.2 1.0 CB A:CYS49 3.3 14.1 1.0 N A:CYS28 3.7 17.7 1.0 N A:CYS46 3.9 11.7 1.0 CA A:CYS28 4.1 19.1 1.0 CA A:CYS46 4.1 12.1 1.0 O A:HOH2011 4.3 18.0 1.0 CA A:CYS25 4.4 13.7 1.0 CB A:ILE27 4.7 15.1 1.0 CA A:CYS49 4.7 13.9 1.0 C A:ILE27 4.8 18.4 1.0 C A:CYS28 4.9 20.0 1.0 C A:CYS25 4.9 14.6 1.0 O A:CYS46 5.0 11.9 1.0 O A:GLU30 5.0 15.7 1.0 N A:PHE29 5.0 19.0 1.0

Zinc binding site 3 out of 4 in the RAD18 Ubiquitin Ligase Ring Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RAD18 Ubiquitin Ligase Ring Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1096 b:21.1 occ:1.00 ND1 B:HIS43 2.0 18.4 1.0 SG B:CYS63 2.3 24.1 1.0 SG B:CYS41 2.3 17.2 1.0 SG B:CYS60 2.3 18.8 1.0 CE1 B:HIS43 2.9 20.5 1.0 CG B:HIS43 3.1 16.4 1.0 CB B:CYS41 3.2 18.8 1.0 CB B:CYS60 3.2 20.7 1.0 CB B:CYS63 3.4 27.1 1.0 CB B:HIS43 3.5 13.2 1.0 N B:CYS63 3.8 26.5 1.0 NE2 B:HIS43 4.1 18.9 1.0 CA B:CYS63 4.1 27.9 1.0 CD2 B:HIS43 4.2 17.4 1.0 CG2 B:VAL65 4.4 24.1 1.0 CA B:CYS41 4.5 18.1 1.0 N B:HIS43 4.5 13.2 1.0 CA B:CYS60 4.6 21.8 1.0 CA B:HIS43 4.6 12.7 1.0 CB B:THR62 4.7 24.1 1.0 O B:CYS41 4.7 16.4 1.0 C B:CYS41 4.7 16.5 1.0 OH B:TYR45 4.7 21.7 1.0 O B:HOH2009 4.7 14.4 1.0 C B:THR62 4.8 27.5 1.0 C B:CYS63 4.9 29.4 1.0 CD1 B:ILE38 5.0 14.5 1.0

Zinc binding site 4 out of 4 in the RAD18 Ubiquitin Ligase Ring Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RAD18 Ubiquitin Ligase Ring Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1097 b:21.7 occ:1.00 SG B:CYS49 2.3 22.0 1.0 SG B:CYS46 2.4 19.0 1.0 SG B:CYS25 2.4 16.1 1.0 SG B:CYS28 2.4 22.4 1.0 CB B:CYS25 3.0 15.1 1.0 CB B:CYS46 3.2 16.5 1.0 CB B:CYS49 3.3 18.6 1.0 CB B:CYS28 3.3 24.5 1.0 N B:CYS28 3.8 22.5 1.0 N B:CYS46 3.9 14.2 1.0 CA B:CYS46 4.1 15.2 1.0 CA B:CYS28 4.1 24.8 1.0 CA B:CYS25 4.5 15.0 1.0 CB B:ILE27 4.5 21.7 1.0 CA B:CYS49 4.7 20.1 1.0 CG2 B:ILE27 4.8 24.2 1.0 C B:ILE27 4.8 23.7 1.0 C B:CYS25 5.0 17.0 1.0 C B:CYS28 5.0 25.0 1.0 N B:CYS49 5.0 19.6 1.0 O B:CYS46 5.0 15.6 1.0

A.Huang, R.G.Hibbert, R.N.De Jong, D.Das, T.K.Sixma, R.Boelens. Symmetry and Asymmetry of the Ring-Ring Dimer of RAD18. J.Mol.Biol. V. 410 424 2011.
ISSN: ISSN 0022-2836
PubMed: 21549715
DOI: 10.1016/J.JMB.2011.04.051