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Cadmium in PDB 4cog: Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia

Enzymatic activity of Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia

All present enzymatic activity of Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia:
3.5.1.9;

Protein crystallography data

The structure of Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia, PDB code: 4cog 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) 134.84 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.859, 50.120, 135.197, 90.00, 94.15, 90.00
R / Rfree (%) 14.886 / 18.431

Other elements in 4cog:

The structure of Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Zinc (Zn) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia (pdb code 4cog). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia, PDB code: 4cog:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 4cog

Go back to Cadmium Binding Sites List in 4cog
Cadmium binding site 1 out of 4 in the Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:13.1
occ:1.00
NE2 A:HIS52 2.2 9.6 1.0
O2 A:GOL1213 2.3 14.6 1.0
OD1 A:ASP54 2.3 11.3 1.0
ND1 A:HIS48 2.3 12.5 1.0
O3 A:GOL1213 2.4 17.5 1.0
OE1 A:GLU172 2.5 13.2 1.0
C3 A:GOL1213 2.9 20.8 1.0
C2 A:GOL1213 3.0 17.8 1.0
CD2 A:HIS52 3.2 10.7 1.0
CE1 A:HIS48 3.2 12.0 1.0
CG A:ASP54 3.2 10.3 1.0
CE1 A:HIS52 3.2 10.1 1.0
ZN A:ZN401 3.3 11.7 1.0
CG A:HIS48 3.4 11.3 1.0
OD2 A:ASP54 3.6 11.1 1.0
CD A:GLU172 3.6 11.4 1.0
CB A:HIS48 3.8 12.8 1.0
O A:PRO147 4.1 13.4 1.0
OE2 A:GLU172 4.1 12.9 1.0
NE2 A:HIS58 4.2 14.9 1.0
O A:HOH2122 4.3 11.9 1.0
CG A:HIS52 4.3 10.0 1.0
C1 A:GOL1213 4.3 18.6 1.0
ND1 A:HIS52 4.4 10.5 1.0
O1 A:GOL1213 4.4 18.0 1.0
NE2 A:HIS48 4.4 12.1 1.0
CA A:HIS48 4.5 13.3 1.0
CD2 A:HIS58 4.5 14.9 1.0
CD2 A:HIS48 4.5 12.9 1.0
CB A:ASP54 4.7 9.6 1.0
CB A:GLU172 4.7 10.6 1.0
CG A:GLU172 4.8 11.2 1.0
O2 A:GOL1212 4.9 36.2 1.0
CE1 A:HIS58 5.0 14.8 1.0

Cadmium binding site 2 out of 4 in 4cog

Go back to Cadmium Binding Sites List in 4cog
Cadmium binding site 2 out of 4 in the Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd402

b:10.7
occ:1.00
NE2 B:HIS52 2.2 7.9 1.0
ND1 B:HIS48 2.3 9.5 1.0
O2 B:GOL1213 2.3 13.1 1.0
O3 B:GOL1213 2.3 14.1 1.0
OD1 B:ASP54 2.4 9.1 1.0
OE1 B:GLU172 2.5 11.8 1.0
C3 B:GOL1213 2.9 19.0 1.0
C2 B:GOL1213 3.0 12.9 1.0
CD2 B:HIS52 3.2 8.0 1.0
CE1 B:HIS48 3.2 10.1 1.0
CE1 B:HIS52 3.2 7.8 1.0
CG B:ASP54 3.3 8.6 1.0
ZN B:ZN401 3.3 9.0 1.0
CG B:HIS48 3.4 8.5 1.0
OD2 B:ASP54 3.6 9.3 1.0
CD B:GLU172 3.6 8.8 1.0
CB B:HIS48 3.8 9.8 1.0
O B:PRO147 4.1 11.1 1.0
O B:HOH2095 4.2 10.4 1.0
OE2 B:GLU172 4.2 10.0 1.0
O1 B:GOL1213 4.2 11.7 1.0
NE2 B:HIS58 4.3 12.8 1.0
C1 B:GOL1213 4.3 17.0 1.0
CG B:HIS52 4.3 7.9 1.0
ND1 B:HIS52 4.3 8.3 1.0
NE2 B:HIS48 4.4 11.4 1.0
CD2 B:HIS48 4.5 10.6 1.0
CA B:HIS48 4.5 10.7 1.0
CD2 B:HIS58 4.5 13.7 1.0
O2 B:GOL1212 4.7 25.5 1.0
CB B:ASP54 4.7 8.2 1.0
CB B:GLU172 4.7 8.2 1.0
CG B:GLU172 4.8 9.1 1.0
CE1 B:HIS58 4.9 13.7 1.0
O B:HIS48 5.0 18.3 1.0

Cadmium binding site 3 out of 4 in 4cog

Go back to Cadmium Binding Sites List in 4cog
Cadmium binding site 3 out of 4 in the Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd402

b:11.3
occ:1.00
O2 C:GOL1213 2.2 10.5 1.0
NE2 C:HIS52 2.3 7.8 1.0
ND1 C:HIS48 2.3 9.2 1.0
OD1 C:ASP54 2.3 9.8 1.0
O3 C:GOL1213 2.4 14.1 1.0
OE1 C:GLU172 2.5 11.3 1.0
C3 C:GOL1213 3.0 17.2 1.0
C2 C:GOL1213 3.0 13.2 1.0
CE1 C:HIS48 3.1 8.8 1.0
CD2 C:HIS52 3.2 8.9 1.0
CG C:ASP54 3.3 10.2 1.0
CE1 C:HIS52 3.3 9.3 1.0
ZN C:ZN401 3.3 9.7 1.0
CG C:HIS48 3.4 9.2 1.0
OD2 C:ASP54 3.6 10.1 1.0
CD C:GLU172 3.6 9.7 1.0
CB C:HIS48 3.8 9.9 1.0
O C:PRO147 4.1 11.7 1.0
OE2 C:GLU172 4.1 11.3 1.0
O C:HOH2104 4.3 10.3 1.0
NE2 C:HIS48 4.3 10.0 1.0
NE2 C:HIS58 4.3 13.6 1.0
CG C:HIS52 4.3 7.9 1.0
C1 C:GOL1213 4.4 16.2 1.0
O1 C:GOL1213 4.4 13.9 1.0
ND1 C:HIS52 4.4 9.5 1.0
CD2 C:HIS48 4.5 10.6 1.0
CA C:HIS48 4.5 12.2 1.0
CD2 C:HIS58 4.5 13.6 1.0
CB C:ASP54 4.7 8.3 1.0
CB C:GLU172 4.7 9.4 1.0
CG C:GLU172 4.8 9.9 1.0
O2 C:GOL1212 4.8 34.1 1.0
O C:HIS48 5.0 16.3 1.0

Cadmium binding site 4 out of 4 in 4cog

Go back to Cadmium Binding Sites List in 4cog
Cadmium binding site 4 out of 4 in the Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Kynurenine Formamidase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd402

b:10.7
occ:1.00
NE2 D:HIS52 2.2 9.0 1.0
O2 D:GOL1214 2.3 11.8 1.0
OD1 D:ASP54 2.3 9.0 1.0
ND1 D:HIS48 2.3 8.3 1.0
O3 D:GOL1214 2.4 14.2 1.0
OE1 D:GLU172 2.5 11.0 1.0
C3 D:GOL1214 3.0 18.2 1.0
C2 D:GOL1214 3.1 13.3 1.0
CE1 D:HIS48 3.2 9.8 1.0
CD2 D:HIS52 3.2 8.1 1.0
CE1 D:HIS52 3.2 9.0 1.0
CG D:ASP54 3.3 9.1 1.0
ZN D:ZN401 3.3 9.8 1.0
CG D:HIS48 3.4 8.9 1.0
CD D:GLU172 3.6 9.5 1.0
OD2 D:ASP54 3.6 10.2 1.0
CB D:HIS48 3.8 9.7 1.0
O D:PRO147 4.1 11.6 1.0
OE2 D:GLU172 4.2 10.4 1.0
NE2 D:HIS58 4.2 11.6 1.0
O D:HOH2073 4.2 11.0 1.0
ND1 D:HIS52 4.3 9.0 1.0
C1 D:GOL1214 4.3 15.6 1.0
CG D:HIS52 4.3 8.2 1.0
NE2 D:HIS48 4.4 9.7 1.0
O1 D:GOL1214 4.4 14.1 1.0
CD2 D:HIS58 4.4 11.0 1.0
CD2 D:HIS48 4.5 10.1 1.0
CA D:HIS48 4.5 10.2 1.0
CB D:ASP54 4.7 8.7 1.0
CB D:GLU172 4.7 7.8 1.0
O2 D:GOL1212 4.8 24.8 1.0
CG D:GLU172 4.8 8.4 1.0
CE1 D:HIS58 4.9 11.3 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 Dec 12 08:24:16 2020

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