Zinc in PDB 3vuy: Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin

The structure of Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin, PDB code: 3vuy was solved by H.Nishimasu, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.68 / 1.98
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	62.438, 62.438, 85.355, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 25.5

The structure of Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin (pdb code 3vuy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin, PDB code: 3vuy:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn801 b:27.4 occ:1.00 SG D:CYS767 2.7 24.2 1.0 SG D:CYS762 2.7 26.8 1.0 SG D:CYS782 2.7 32.3 1.0 SG D:CYS779 2.8 26.1 1.0 CB D:CYS762 3.1 24.5 1.0 CB D:CYS782 3.3 24.6 1.0 CB D:CYS767 3.4 26.2 1.0 CB D:CYS779 3.4 34.3 1.0 N D:CYS779 3.9 32.4 1.0 CB D:ALA764 4.2 30.1 1.0 CB D:HIS769 4.2 22.4 1.0 CA D:CYS779 4.3 24.7 1.0 NH1 A:ARG72 4.4 32.7 1.0 ND1 D:HIS769 4.4 22.3 1.0 N D:CYS782 4.5 23.9 1.0 CA D:CYS782 4.5 27.4 1.0 CA D:CYS762 4.6 29.7 1.0 CG D:HIS769 4.7 26.1 1.0 CA D:CYS767 4.9 26.1 1.0 NH2 A:ARG72 4.9 31.1 1.0 C D:CYS779 4.9 30.4 1.0 O D:CYS779 5.0 29.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn801 b:34.5 occ:1.00 SG F:CYS767 2.7 27.2 1.0 SG F:CYS762 2.7 35.3 1.0 SG F:CYS779 2.8 35.2 1.0 SG F:CYS782 2.8 42.2 1.0 CB F:CYS762 3.2 30.8 1.0 CB F:CYS782 3.3 31.1 1.0 CB F:CYS779 3.4 44.5 1.0 CB F:CYS767 3.5 32.1 1.0 N F:CYS779 3.9 31.8 1.0 CB F:HIS769 4.1 26.3 1.0 CB F:ALA764 4.2 33.4 1.0 CA F:CYS779 4.3 30.8 1.0 NH1 C:ARG72 4.3 31.1 1.0 CA F:CYS782 4.5 31.5 1.0 N F:CYS782 4.5 30.5 1.0 ND1 F:HIS769 4.6 25.5 1.0 CA F:CYS762 4.7 43.6 1.0 CG F:HIS769 4.7 33.0 1.0 NH2 C:ARG72 4.9 32.9 1.0 CA F:CYS767 4.9 35.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A20 ZF7 in Complex with Linear Tetraubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn801 b:34.6 occ:1.00 SG E:CYS767 2.7 33.0 1.0 SG E:CYS762 2.7 33.8 1.0 SG E:CYS782 2.8 40.0 1.0 SG E:CYS779 2.8 37.4 1.0 CB E:CYS762 3.1 31.4 1.0 CB E:CYS782 3.3 26.6 1.0 CB E:CYS779 3.4 28.9 1.0 CB E:CYS767 3.6 32.2 1.0 N E:CYS779 3.9 25.5 1.0 CB E:HIS769 4.1 30.0 1.0 CA E:CYS779 4.2 25.2 1.0 CB E:ALA764 4.3 42.8 1.0 NH1 B:ARG72 4.4 44.6 1.0 N E:CYS782 4.4 28.7 1.0 CA E:CYS782 4.5 36.6 1.0 ND1 E:HIS769 4.5 28.9 1.0 CA E:CYS762 4.6 39.4 1.0 NH2 B:ARG72 4.7 45.2 1.0 CG E:HIS769 4.7 34.1 1.0 C E:CYS779 4.9 35.2 1.0 CA E:CYS767 5.0 34.6 1.0

F.Tokunaga, H.Nishimasu, R.Ishitani, E.Goto, T.Noguchi, K.Mio, K.Kamei, A.Ma, K.Iwai, O.Nureki. Specific Recognition of Linear Polyubiquitin By A20 Zinc Finger 7 Is Involved in Nf-Kappab Regulation Embo J. V. 31 3856 2012.
ISSN: ISSN 0261-4189
PubMed: 23032187
DOI: 10.1038/EMBOJ.2012.241