Zinc in PDB 4xkl: Crystal Structure of NDP52 ZF2 in Complex with Mono-Ubiquitin

The structure of Crystal Structure of NDP52 ZF2 in Complex with Mono-Ubiquitin, PDB code: 4xkl was solved by X.Xie, F.Li, Y.Wang, Z.Lin, X.Chen, J.Liu, L.Pan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.90 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.950, 73.800, 39.700, 90.00, 108.49, 90.00
R / Rfree (%)	19.4 / 24.3

The binding sites of Zinc atom in the Crystal Structure of NDP52 ZF2 in Complex with Mono-Ubiquitin (pdb code 4xkl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of NDP52 ZF2 in Complex with Mono-Ubiquitin, PDB code: 4xkl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of NDP52 ZF2 in Complex with Mono-Ubiquitin


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 NDP52 ZF2 in Complex with Mono-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:14.2 occ:1.00 NE2 B:HIS440 2.0 17.1 1.0 SG B:CYS425 2.1 16.5 1.0 NE2 B:HIS444 2.3 18.9 1.0 SG B:CYS422 2.3 19.0 1.0 CE1 B:HIS440 2.8 15.7 1.0 CD2 B:HIS444 3.1 15.0 1.0 CB B:CYS422 3.1 17.3 1.0 CB B:CYS425 3.1 16.3 1.0 CD2 B:HIS440 3.2 18.2 1.0 CE1 B:HIS444 3.4 18.8 1.0 N B:CYS425 3.7 25.4 1.0 CA B:CYS425 3.9 19.8 1.0 ND1 B:HIS440 4.0 17.8 1.0 CG B:HIS440 4.2 16.4 1.0 CG B:HIS444 4.3 13.3 1.0 ND1 B:HIS444 4.4 14.7 1.0 CB B:ILE424 4.5 29.7 1.0 CA B:CYS422 4.6 22.1 1.0 C B:ILE424 4.6 23.5 1.0 C B:CYS425 4.6 19.9 1.0 CB B:LYS427 4.7 28.3 1.0 N B:ASP426 4.8 24.1 1.0 N B:ILE424 4.9 32.6 1.0 CA B:ILE424 4.9 29.3 1.0 N B:LYS427 4.9 34.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of NDP52 ZF2 in Complex with Mono-Ubiquitin


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 NDP52 ZF2 in Complex with Mono-Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:15.3 occ:1.00 NE2 D:HIS440 1.9 13.2 1.0 NE2 D:HIS444 2.2 15.3 1.0 SG D:CYS422 2.3 17.3 1.0 SG D:CYS425 2.3 16.5 1.0 CE1 D:HIS440 2.8 14.5 1.0 CD2 D:HIS440 3.1 13.4 1.0 CB D:CYS422 3.1 25.6 1.0 CD2 D:HIS444 3.1 14.1 1.0 CE1 D:HIS444 3.2 14.9 1.0 CB D:CYS425 3.3 16.4 1.0 N D:CYS425 3.7 18.0 1.0 ND1 D:HIS440 4.0 12.7 1.0 CA D:CYS425 4.0 19.4 1.0 CG D:HIS440 4.1 14.5 1.0 CG D:HIS444 4.3 17.4 1.0 ND1 D:HIS444 4.3 17.6 1.0 CB D:ILE424 4.4 24.9 1.0 CA D:CYS422 4.5 28.4 1.0 C D:ILE424 4.6 22.2 1.0 CB D:LYS427 4.7 20.5 1.0 C D:CYS425 4.7 21.2 1.0 N D:ASP426 4.7 21.0 1.0 N D:ILE424 4.8 27.9 1.0 CD2 C:LEU8 4.8 25.6 1.0 CA D:ILE424 4.9 20.3 1.0 C D:CYS422 4.9 24.7 1.0 N D:LYS427 4.9 26.4 1.0

X.Xie, F.Li, Y.Wang, Y.Wang, Z.Lin, X.Cheng, J.Liu, C.Chen, L.Pan. Molecular Basis of Ubiquitin Recognition By the Autophagy Receptor CALCOCO2 Autophagy V. 11 1775 2015.
ISSN: ESSN 1554-8635
PubMed: 26506893
DOI: 10.1080/15548627.2015.1082025