Zinc in PDB 3vuw: Crystal Structure of A20 ZF7 in Complex with Linear Ubiquitin, Form I

The structure of Crystal Structure of A20 ZF7 in Complex with Linear Ubiquitin, Form I, PDB code: 3vuw 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)	41.50 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.173, 51.991, 52.180, 70.08, 80.25, 78.05
R / Rfree (%)	17.8 / 22.2

The structure of Crystal Structure of A20 ZF7 in Complex with Linear Ubiquitin, Form I 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 Ubiquitin, Form I (pdb code 3vuw). 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 Ubiquitin, Form I, PDB code: 3vuw:
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 Ubiquitin, Form I


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 Ubiquitin, Form I within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn801 b:24.6 occ:1.00 SG E:CYS782 2.4 22.0 1.0 SG E:CYS767 2.4 23.8 1.0 SG E:CYS762 2.4 22.7 1.0 SG E:CYS779 2.5 22.3 1.0 CB E:CYS762 3.0 20.9 1.0 CB E:CYS767 3.2 20.8 1.0 CB E:CYS782 3.2 18.1 1.0 CB E:CYS779 3.6 18.3 1.0 N E:CYS779 4.0 21.4 1.0 CB E:ALA764 4.1 20.5 1.0 CB E:HIS769 4.2 22.8 1.0 N E:CYS782 4.3 24.5 1.0 NH1 C:ARG72 4.3 21.7 1.0 CA E:CYS782 4.3 24.9 1.0 CA E:CYS779 4.4 19.9 1.0 CD2 E:HIS769 4.4 16.6 1.0 CA E:CYS762 4.5 23.4 1.0 CG E:HIS769 4.6 20.6 1.0 CA E:CYS767 4.6 24.3 1.0 O C:HOH102 4.9 23.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of A20 ZF7 in Complex with Linear Ubiquitin, Form I


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 Ubiquitin, Form I within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn801 b:28.6 occ:1.00 SG F:CYS782 2.4 27.8 1.0 SG F:CYS762 2.4 27.1 1.0 SG F:CYS767 2.4 25.7 1.0 SG F:CYS779 2.5 29.1 1.0 CB F:CYS782 3.1 26.4 1.0 CB F:CYS762 3.2 27.9 1.0 CB F:CYS767 3.3 23.1 1.0 CB F:CYS779 3.4 29.7 1.0 N F:CYS779 4.0 25.8 1.0 CB F:HIS769 4.3 26.1 1.0 CB F:ALA764 4.3 27.4 1.0 CA F:CYS782 4.3 31.4 1.0 N F:CYS782 4.3 26.7 1.0 CA F:CYS779 4.3 31.6 1.0 CD2 F:HIS769 4.3 22.0 1.0 NH2 B:ARG72 4.4 28.3 1.0 CG F:HIS769 4.6 25.1 1.0 CA F:CYS762 4.7 30.4 1.0 CA F:CYS767 4.7 27.6 1.0 C F:CYS779 5.0 31.7 1.0 O F:CYS779 5.0 29.3 1.0 NH1 B:ARG72 5.0 31.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of A20 ZF7 in Complex with Linear Ubiquitin, Form I


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 Ubiquitin, Form I within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn801 b:29.7 occ:1.00 SG G:CYS762 2.4 29.1 1.0 SG G:CYS767 2.4 27.7 1.0 SG G:CYS779 2.5 24.3 1.0 SG G:CYS782 2.5 26.9 1.0 CB G:CYS762 3.2 32.6 1.0 CB G:CYS782 3.2 23.9 1.0 CB G:CYS767 3.3 25.7 1.0 CB G:CYS779 3.6 22.2 1.0 N G:CYS779 4.0 24.2 1.0 CB G:ALA764 4.3 28.7 1.0 N G:CYS782 4.3 30.2 1.0 CB G:HIS769 4.3 22.4 1.0 NH1 A:ARG72 4.3 26.9 1.0 CA G:CYS779 4.3 29.4 1.0 CA G:CYS782 4.3 29.6 1.0 CD2 G:HIS769 4.4 16.3 1.0 CG G:HIS769 4.6 22.9 1.0 CA G:CYS762 4.6 35.4 1.0 CA G:CYS767 4.7 26.7 1.0 C G:CYS779 5.0 32.7 1.0 NH2 A:ARG72 5.0 24.6 1.0 N G:ALA764 5.0 33.4 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