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

The structure of Crystal Structure of A20 ZF7 in Complex with Linear Ubiquitin, Form II, PDB code: 3vux 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)	26.99 / 1.70
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	62.329, 62.329, 85.180, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 20.3

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn801 b:19.3 occ:1.00 SG E:CYS767 2.4 15.9 1.0 SG E:CYS762 2.4 19.8 1.0 SG E:CYS779 2.5 21.3 1.0 SG E:CYS782 2.6 21.0 1.0 CB E:CYS762 3.2 19.8 1.0 CB E:CYS782 3.2 17.7 1.0 CB E:CYS767 3.4 21.6 1.0 CB E:CYS779 3.6 16.0 1.0 N E:CYS779 4.0 18.3 1.0 CB E:HIS769 4.2 19.4 1.0 O B:HOH132 4.2 49.9 1.0 CB E:ALA764 4.3 18.7 1.0 CA E:CYS779 4.4 18.1 1.0 CA E:CYS782 4.4 22.1 1.0 N E:CYS782 4.4 23.2 1.0 ND1 E:HIS769 4.4 17.1 1.0 NH1 B:ARG72 4.5 26.2 1.0 CA E:CYS762 4.6 20.2 1.0 CG E:HIS769 4.7 16.1 1.0 CA E:CYS767 4.8 22.2 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn801 b:21.3 occ:1.00 SG F:CYS767 2.5 20.6 1.0 SG F:CYS782 2.5 27.5 1.0 SG F:CYS762 2.5 21.0 1.0 SG F:CYS779 2.6 19.8 1.0 CB F:CYS782 3.2 16.0 1.0 CB F:CYS762 3.2 19.0 1.0 CB F:CYS767 3.4 18.6 1.0 CB F:CYS779 3.6 15.1 1.0 N F:CYS779 4.0 18.5 1.0 CB F:HIS769 4.2 18.2 1.0 ND1 F:HIS769 4.3 17.5 1.0 CA F:CYS782 4.4 21.0 1.0 CA F:CYS779 4.4 14.7 1.0 CB F:ALA764 4.4 27.4 1.0 N F:CYS782 4.4 19.1 1.0 NH1 C:ARG72 4.5 27.6 1.0 CG F:HIS769 4.6 17.9 1.0 CA F:CYS762 4.6 20.5 1.0 O C:HOH147 4.7 32.5 1.0 CA F:CYS767 4.8 21.8 1.0

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


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 II within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn801 b:20.7 occ:1.00 SG G:CYS767 2.5 20.6 1.0 SG G:CYS762 2.5 17.3 1.0 SG G:CYS779 2.5 20.8 1.0 SG G:CYS782 2.6 24.6 1.0 CB G:CYS762 3.1 25.8 1.0 CB G:CYS782 3.2 22.7 1.0 CB G:CYS767 3.4 16.7 1.0 CB G:CYS779 3.6 30.4 1.0 N G:CYS779 3.8 17.4 1.0 CB G:HIS769 4.1 20.4 1.0 CB G:ALA764 4.1 25.9 1.0 N G:CYS782 4.3 16.5 1.0 CA G:CYS779 4.3 16.5 1.0 CA G:CYS782 4.4 16.9 1.0 ND1 G:HIS769 4.4 21.9 1.0 NH1 A:ARG72 4.4 26.7 1.0 CA G:CYS762 4.6 25.0 1.0 CG G:HIS769 4.6 20.9 1.0 NH2 A:ARG72 4.7 32.3 1.0 CA G:CYS767 4.8 22.2 1.0 C G:TYR778 4.9 22.0 1.0 C G:CYS779 5.0 19.8 1.0 O G:CYS779 5.0 18.2 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