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Zinc in PDB 4cz1: Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.

Enzymatic activity of Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.

All present enzymatic activity of Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.:
3.5.1.9;

Protein crystallography data

The structure of Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone., PDB code: 4cz1 was solved by L.Diaz-Saez, V.Srikannathasan, M.Zoltner, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.64 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.695, 66.561, 84.061, 90.00, 90.24, 90.00
R / Rfree (%) 18.37 / 22.41

Other elements in 4cz1:

The structure of Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone. also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone. (pdb code 4cz1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone., PDB code: 4cz1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4cz1

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Zinc binding site 1 out of 8 in the Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.


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 Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:29.7
occ:1.00
 OD2 A:ASP56 2.0 9.0 1.0
O A:HOH2103 2.2 33.9 1.0
OE2 A:GLU173 2.2 15.2 1.0
NE2 A:HIS161 2.2 12.2 1.0
O A:HOH2046 2.2 16.4 1.0
OE1 A:GLU173 2.7 13.3 1.0
CD A:GLU173 2.8 13.1 1.0
CG A:ASP56 3.0 9.8 1.0
ZN A:ZN402 3.1 25.2 1.0
CE1 A:HIS161 3.1 11.5 1.0
CD2 A:HIS161 3.3 12.4 1.0
OD1 A:ASP56 3.3 12.2 1.0
O A:HOH2027 3.8 4.0 1.0
CG A:GLU173 4.2 11.9 1.0
ND1 A:HIS161 4.3 11.9 1.0
CD2 A:HIS60 4.3 12.2 1.0
NE2 A:HIS60 4.3 12.0 1.0
CB A:ASP56 4.3 9.4 1.0
OG A:SER149 4.4 12.1 1.0
CG A:HIS161 4.4 12.2 1.0
NAJ A:VNJ501 4.4 47.4 1.0
O A:PRO148 4.4 13.7 1.0
CA A:SER149 4.7 12.8 1.0
CG2 A:ILE171 4.7 12.9 1.0
N A:VAL150 4.9 11.0 1.0
ND1 A:HIS50 4.9 9.2 1.0
CB A:SER149 5.0 11.9 1.0

Zinc binding site 2 out of 8 in 4cz1

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Zinc binding site 2 out of 8 in the Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.


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 Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:25.2
occ:1.00
 OD1 A:ASP56 2.2 12.2 1.0
ND1 A:HIS50 2.3 9.2 1.0
O A:HOH2027 2.3 4.0 1.0
NE2 A:HIS54 2.4 5.5 1.0
O A:HOH2046 2.5 16.4 1.0
OE1 A:GLU173 2.5 13.3 1.0
CD2 A:HIS54 3.0 5.5 1.0
CE1 A:HIS50 3.1 8.6 1.0
CG A:ASP56 3.1 9.8 1.0
ZN A:ZN401 3.1 29.7 1.0
CG A:HIS50 3.3 8.9 1.0
OD2 A:ASP56 3.4 9.0 1.0
CE1 A:HIS54 3.6 5.4 1.0
CD A:GLU173 3.7 13.1 1.0
CB A:HIS50 3.7 8.6 1.0
NE2 A:HIS50 4.2 8.6 1.0
OE2 A:GLU173 4.3 15.2 1.0
CG A:HIS54 4.3 5.8 1.0
NE2 A:HIS60 4.4 12.0 1.0
CD2 A:HIS50 4.4 8.9 1.0
CB A:ASP56 4.5 9.4 1.0
O A:HOH2103 4.5 33.9 1.0
ND1 A:HIS54 4.5 5.6 1.0
CA A:HIS50 4.6 9.1 1.0
CD2 A:HIS60 4.6 12.2 1.0
NAJ A:VNJ501 4.6 47.4 1.0
O A:PRO148 4.6 13.7 1.0
OAI A:VNJ501 4.8 47.5 1.0
CG A:GLU173 4.8 11.9 1.0
CA A:ASP56 4.8 9.1 1.0
N A:ASP56 4.8 9.4 1.0
CB A:GLU173 5.0 11.0 1.0

Zinc binding site 3 out of 8 in 4cz1

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Zinc binding site 3 out of 8 in the Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.


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 Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:22.1
occ:1.00
 OE2 B:GLU173 2.1 13.8 1.0
OD2 B:ASP56 2.1 13.8 1.0
NE2 B:HIS161 2.2 17.9 1.0
O B:HOH2022 2.2 10.8 1.0
O B:HOH2053 2.6 31.7 1.0
OE1 B:GLU173 2.6 13.9 1.0
CD B:GLU173 2.6 13.0 1.0
CE1 B:HIS161 3.1 20.5 1.0
CG B:ASP56 3.1 12.8 1.0
ZN B:ZN402 3.1 23.5 1.0
CD2 B:HIS161 3.3 17.2 1.0
OD1 B:ASP56 3.4 13.1 1.0
O B:HOH2016 4.0 18.0 1.0
CG B:GLU173 4.1 13.0 1.0
ND1 B:HIS161 4.2 20.0 1.0
OG B:SER149 4.3 15.5 1.0
CG B:HIS161 4.4 18.5 1.0
O B:PRO148 4.4 14.0 1.0
CB B:ASP56 4.4 11.6 1.0
CA B:SER149 4.6 16.1 1.0
CG2 B:ILE171 4.6 14.3 1.0
CD2 B:HIS60 4.7 20.1 1.0
N B:VAL150 4.8 17.0 1.0
NE2 B:HIS60 4.8 20.6 1.0
CB B:SER149 4.9 16.9 1.0
ND1 B:HIS50 5.0 12.3 1.0

Zinc binding site 4 out of 8 in 4cz1

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Zinc binding site 4 out of 8 in the Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:23.5
occ:1.00
 NE2 B:HIS54 2.3 9.4 1.0
OE1 B:GLU173 2.3 13.9 1.0
O B:HOH2022 2.3 10.8 1.0
OD1 B:ASP56 2.3 13.1 1.0
ND1 B:HIS50 2.4 12.3 1.0
O B:HOH2016 2.4 18.0 1.0
CD2 B:HIS54 3.0 9.8 1.0
ZN B:ZN401 3.1 22.1 1.0
CG B:ASP56 3.2 12.8 1.0
CE1 B:HIS50 3.3 13.3 1.0
CE1 B:HIS54 3.4 9.6 1.0
CG B:HIS50 3.4 13.1 1.0
CD B:GLU173 3.4 13.0 1.0
OD2 B:ASP56 3.5 13.8 1.0
CB B:HIS50 3.7 14.2 1.0
O B:HOH2053 3.9 31.7 1.0
OE2 B:GLU173 4.1 13.8 1.0
CG B:HIS54 4.3 9.4 1.0
O B:PRO148 4.4 14.0 1.0
ND1 B:HIS54 4.4 10.2 1.0
NE2 B:HIS50 4.5 13.5 1.0
CA B:HIS50 4.5 15.6 1.0
CD2 B:HIS50 4.5 13.1 1.0
CG B:GLU173 4.5 13.0 1.0
CB B:ASP56 4.6 11.6 1.0
CB B:GLU173 4.7 12.1 1.0
NE2 B:HIS60 4.9 20.6 1.0
CD2 B:HIS60 5.0 20.1 1.0

Zinc binding site 5 out of 8 in 4cz1

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Zinc binding site 5 out of 8 in the Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:34.0
occ:1.00
 OD2 C:ASP56 2.1 11.2 1.0
OE2 C:GLU173 2.1 14.6 1.0
NE2 C:HIS161 2.3 18.6 1.0
O C:HOH2055 2.3 10.2 1.0
O C:HOH2092 2.5 19.2 1.0
OE1 C:GLU173 2.6 13.9 1.0
CD C:GLU173 2.6 14.9 1.0
CG C:ASP56 3.1 9.6 1.0
CE1 C:HIS161 3.1 17.8 1.0
ZN C:ZN402 3.2 28.7 1.0
OD1 C:ASP56 3.3 11.1 1.0
CD2 C:HIS161 3.3 19.9 1.0
O C:HOH2024 3.8 10.6 1.0
CG C:GLU173 4.0 14.4 1.0
ND1 C:HIS161 4.3 17.4 1.0
O C:PRO148 4.3 13.5 1.0
OG C:SER149 4.3 14.7 1.0
CB C:ASP56 4.4 9.0 1.0
NE2 C:HIS60 4.4 10.2 1.0
CD2 C:HIS60 4.4 10.0 1.0
CG C:HIS161 4.4 19.6 1.0
CA C:SER149 4.6 15.0 1.0
CG2 C:ILE171 4.7 16.9 1.0
N C:VAL150 4.8 17.1 1.0
CB C:SER149 4.9 15.4 1.0
ND1 C:HIS50 5.0 10.5 1.0

Zinc binding site 6 out of 8 in 4cz1

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Zinc binding site 6 out of 8 in the Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:28.7
occ:1.00
 O C:HOH2055 2.0 10.2 1.0
ND1 C:HIS50 2.2 10.5 1.0
OD1 C:ASP56 2.2 11.1 1.0
NE2 C:HIS54 2.3 7.2 1.0
O C:HOH2024 2.4 10.6 1.0
OE1 C:GLU173 2.4 13.9 1.0
CD2 C:HIS54 3.0 6.8 1.0
CE1 C:HIS50 3.1 10.7 1.0
ZN C:ZN401 3.2 34.0 1.0
CG C:ASP56 3.2 9.6 1.0
CG C:HIS50 3.3 10.7 1.0
OD2 C:ASP56 3.5 11.2 1.0
CE1 C:HIS54 3.5 7.0 1.0
CD C:GLU173 3.6 14.9 1.0
CB C:HIS50 3.7 11.0 1.0
O C:HOH2092 4.0 19.2 1.0
NE2 C:HIS50 4.3 10.5 1.0
CG C:HIS54 4.3 7.2 1.0
OE2 C:GLU173 4.3 14.6 1.0
CD2 C:HIS50 4.4 11.0 1.0
NE2 C:HIS60 4.4 10.2 1.0
ND1 C:HIS54 4.5 6.8 1.0
CA C:HIS50 4.5 10.5 1.0
CB C:ASP56 4.5 9.0 1.0
O C:PRO148 4.6 13.5 1.0
CD2 C:HIS60 4.6 10.0 1.0
CG C:GLU173 4.7 14.4 1.0
CB C:GLU173 4.9 12.9 1.0
CA C:ASP56 4.9 9.3 1.0

Zinc binding site 7 out of 8 in 4cz1

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Zinc binding site 7 out of 8 in the Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:20.3
occ:1.00
 OD2 D:ASP56 2.1 12.2 1.0
OE2 D:GLU173 2.1 14.7 1.0
NE2 D:HIS161 2.2 11.3 1.0
O D:HOH2033 2.3 7.6 1.0
OE1 D:GLU173 2.6 13.7 1.0
CD D:GLU173 2.7 14.7 1.0
CE1 D:HIS161 3.0 10.9 1.0
ZN D:ZN402 3.1 20.4 1.0
CG D:ASP56 3.1 10.8 1.0
CD2 D:HIS161 3.2 11.9 1.0
OD1 D:ASP56 3.4 11.2 1.0
O D:HOH2022 3.9 7.3 1.0
O D:HOH2037 4.1 33.3 1.0
CG D:GLU173 4.1 12.0 1.0
ND1 D:HIS161 4.2 11.6 1.0
CG D:HIS161 4.3 12.4 1.0
OG D:SER149 4.4 10.4 1.0
O D:PRO148 4.4 14.4 1.0
CB D:ASP56 4.4 10.2 1.0
CD2 D:HIS60 4.6 17.6 1.0
CA D:SER149 4.6 11.6 1.0
CG2 D:ILE171 4.7 11.9 1.0
NE2 D:HIS60 4.7 17.4 1.0
N D:VAL150 4.8 11.0 1.0
CB D:SER149 4.9 10.5 1.0
ND1 D:HIS50 5.0 14.8 1.0

Zinc binding site 8 out of 8 in 4cz1

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Zinc binding site 8 out of 8 in the Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Kynurenine Formamidase From Bacillus Anthracis Complexed with 2-Aminoacetophenone. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:20.4
occ:1.00
 O D:HOH2033 2.2 7.6 1.0
OD1 D:ASP56 2.2 11.2 1.0
OE1 D:GLU173 2.3 13.7 1.0
O D:HOH2022 2.4 7.3 1.0
NE2 D:HIS54 2.4 5.4 1.0
ND1 D:HIS50 2.4 14.8 1.0
ZN D:ZN401 3.1 20.3 1.0
CG D:ASP56 3.1 10.8 1.0
CD2 D:HIS54 3.1 5.7 1.0
CE1 D:HIS50 3.3 15.4 1.0
OD2 D:ASP56 3.3 12.2 1.0
CG D:HIS50 3.4 14.3 1.0
CD D:GLU173 3.5 14.7 1.0
CE1 D:HIS54 3.5 5.5 1.0
CB D:HIS50 3.8 13.2 1.0
OE2 D:GLU173 4.1 14.7 1.0
O D:HOH2037 4.2 33.3 1.0
CG D:HIS54 4.4 5.5 1.0
NE2 D:HIS50 4.4 15.9 1.0
O D:PRO148 4.5 14.4 1.0
CB D:ASP56 4.5 10.2 1.0
ND1 D:HIS54 4.5 5.5 1.0
CD2 D:HIS50 4.5 14.5 1.0
CA D:HIS50 4.6 13.2 1.0
CG D:GLU173 4.6 12.0 1.0
NE2 D:HIS60 4.7 17.4 1.0
CD2 D:HIS60 4.7 17.6 1.0
CB D:GLU173 4.8 10.5 1.0
CA D:ASP56 4.9 10.3 1.0
N D:ASP56 4.9 10.2 1.0
O D:HOH2023 5.0 22.0 1.0

Reference:

L.Diaz-Saez, V.Srikannathasan, M.Zoltner, W.N.Hunter. Structure of Bacterial Kynurenine Formamidase Reveals A Crowded Binuclear-Zinc Catalytic Site Primed to Generate A Potent Nucleophile. Biochem.J. V. 462 581 2014.
ISSN: ISSN 0264-6021
PubMed: 24942958
DOI: 10.1042/BJ20140511
Page generated: Sat Oct 26 21:12:12 2024

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