Zinc in PDB 6uxu: X-Ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation

The structure of X-Ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation, PDB code: 6uxu was solved by D.S.Catlin, D.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.02 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.802, 105.182, 122.422, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.8

The binding sites of Zinc atom in the X-Ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation (pdb code 6uxu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the X-Ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation, PDB code: 6uxu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the X-Ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:16.5 occ:0.74 O A:HOH541 1.9 10.7 1.0 NE2 A:HIS257 2.0 14.1 1.0 NE2 A:HIS117 2.1 13.2 1.0 OD1 A:ASN216 2.3 21.1 1.0 OD2 A:ASP116 2.3 16.2 1.0 CD2 A:HIS117 2.9 12.2 1.0 CE1 A:HIS257 2.9 16.3 1.0 CD2 A:HIS257 3.0 14.8 1.0 CG A:ASN216 3.1 27.3 1.0 CE1 A:HIS117 3.1 14.3 1.0 CG A:ASP116 3.2 17.4 1.0 ND2 A:ASN216 3.2 30.8 1.0 OD1 A:ASP116 3.4 14.6 1.0 O A:HOH670 3.5 45.9 1.0 ND1 A:HIS257 4.1 16.2 1.0 CG A:HIS117 4.1 13.0 1.0 CG A:HIS257 4.2 15.2 1.0 ND1 A:HIS117 4.2 14.3 1.0 CG2 A:THR66 4.5 16.8 1.0 CB A:ASN216 4.5 19.5 1.0 OG1 A:THR66 4.6 17.1 1.0 CB A:ASP116 4.6 14.9 1.0 O A:HOH687 4.9 44.4 1.0 CB A:HIS114 4.9 19.9 1.0 O A:GLY256 4.9 15.1 1.0

Zinc binding site 2 out of 3 in the X-Ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:23.6 occ:0.65 ND1 B:HIS143 2.0 27.5 1.0 ND1 A:HIS143 2.0 26.4 1.0 OD1 B:ASP146 2.1 31.7 1.0 OD2 A:ASP146 2.3 43.6 1.0 OD1 A:ASP146 2.7 38.7 1.0 CG A:ASP146 2.8 40.9 1.0 CG B:ASP146 2.9 37.0 1.0 CG B:HIS143 3.0 23.1 1.0 CE1 B:HIS143 3.0 30.1 1.0 CG A:HIS143 3.0 24.4 1.0 CE1 A:HIS143 3.0 28.6 1.0 CB A:HIS143 3.3 21.2 1.0 CB B:HIS143 3.3 18.4 1.0 OD2 B:ASP146 3.5 45.6 1.0 CB B:ASP146 3.8 34.6 1.0 CA B:HIS143 3.9 18.9 1.0 CA A:HIS143 4.0 20.4 1.0 NE2 B:HIS143 4.1 26.2 1.0 NE2 A:HIS143 4.1 26.2 1.0 CD2 B:HIS143 4.1 24.6 1.0 CD2 A:HIS143 4.1 24.0 1.0 CB A:ASP146 4.2 37.8 1.0 O B:GLY142 4.3 20.2 1.0 O A:GLY142 4.4 25.9 1.0 O A:HIS143 4.8 18.0 1.0 O B:HIS143 4.8 16.8 1.0 C B:GLY142 4.9 20.1 1.0 N B:HIS143 4.9 17.0 1.0 C A:HIS143 4.9 20.8 1.0 C B:HIS143 4.9 16.4 1.0 N A:HIS143 4.9 20.9 1.0 C A:GLY142 5.0 25.2 1.0

Zinc binding site 3 out of 3 in the X-Ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of Chlorothalonil Dehalogenase: Analyzing the Catalytic Mechanism of Hydrolytic Dehalogenation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:12.6 occ:0.70 O B:HOH523 2.0 8.5 1.0 NE2 B:HIS117 2.1 17.5 1.0 NE2 B:HIS257 2.1 15.7 1.0 OD1 B:ASN216 2.2 17.7 1.0 OD2 B:ASP116 2.4 14.1 1.0 CD2 B:HIS117 2.9 14.1 1.0 CG B:ASN216 2.9 26.0 1.0 CE1 B:HIS257 3.0 15.3 1.0 ND2 B:ASN216 3.0 40.7 1.0 CD2 B:HIS257 3.1 12.0 1.0 CE1 B:HIS117 3.1 16.8 1.0 CG B:ASP116 3.3 16.9 1.0 OD1 B:ASP116 3.4 15.8 1.0 CG B:HIS117 4.1 14.7 1.0 ND1 B:HIS257 4.1 15.7 1.0 ND1 B:HIS117 4.2 14.0 1.0 CG B:HIS257 4.2 12.4 1.0 CB B:ASN216 4.4 19.8 1.0 OG1 B:THR66 4.5 14.5 1.0 CG2 B:THR66 4.6 12.5 1.0 ND1 B:HIS114 4.7 33.0 1.0 CB B:ASP116 4.7 12.6 1.0 CB B:HIS114 4.9 12.8 1.0 O B:HOH671 4.9 41.9 1.0 O B:GLY256 4.9 11.0 1.0 CA B:ASN216 5.0 15.3 1.0 O B:HOH662 5.0 42.6 1.0

D.S.Catlin, X.Yang, B.Bennett, R.C.Holz, D.Liu. Structural Basis For the Hydrolytic Dehalogenation of the Fungicide Chlorothalonil. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32358058
DOI: 10.1074/JBC.RA120.013150