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

Protein crystallography data

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

Zinc Binding Sites:

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 6uxu

Go back to Zinc Binding Sites List in 6uxu
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 6uxu

Go back to Zinc Binding Sites List in 6uxu
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 6uxu

Go back to Zinc Binding Sites List in 6uxu
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

Reference:

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
Page generated: Wed Dec 16 13:00:28 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy