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

Protein crystallography data

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

Zinc Binding Sites:

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 4xkl

Go back to Zinc Binding Sites List in 4xkl
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 4xkl

Go back to Zinc Binding Sites List in 4xkl
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

Reference:

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
Page generated: Wed Dec 16 05:54:31 2020

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