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Copper in PDB 1gqg: Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate

Enzymatic activity of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate

All present enzymatic activity of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate:
1.13.11.24;

Protein crystallography data

The structure of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate, PDB code: 1gqg was solved by R.A.Steiner, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 108.939, 55.646, 123.863, 90.00, 98.26, 90.00
R / Rfree (%) 16.1 / 18.3

Copper Binding Sites:

The binding sites of Copper atom in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate (pdb code 1gqg). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate, PDB code: 1gqg:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1gqg

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Copper binding site 1 out of 4 in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1352

b:17.5
occ:1.00
NE2 A:HIS68 2.1 14.0 1.0
NE2 A:HIS112 2.2 13.0 1.0
NE2 A:HIS66 2.2 16.1 1.0
S1 A:DCD1351 2.2 18.9 1.0
S2 A:DCD1351 2.8 20.2 1.0
C1 A:DCD1351 2.9 17.5 1.0
CE1 A:HIS68 3.0 15.4 1.0
CD2 A:HIS68 3.0 13.9 1.0
CE1 A:HIS112 3.1 14.9 1.0
CE1 A:HIS66 3.1 14.3 1.0
CD2 A:HIS66 3.1 14.8 1.0
CD2 A:HIS112 3.2 14.7 1.0
ND1 A:HIS68 4.1 14.4 1.0
CG A:HIS68 4.2 13.8 1.0
ND1 A:HIS112 4.2 12.8 1.0
N1 A:DCD1351 4.2 18.1 1.0
ND1 A:HIS66 4.2 14.3 1.0
CG A:HIS66 4.3 14.2 1.0
CG A:HIS112 4.3 12.4 1.0
CG A:GLU73 4.6 17.1 1.0
OE1 A:GLU73 4.6 22.0 1.0
CD A:GLU73 4.7 20.1 1.0
CZ A:PHE132 4.8 28.4 1.0
C3 A:DCD1351 5.0 18.4 1.0
CE2 A:PHE132 5.0 28.2 1.0

Copper binding site 2 out of 4 in 1gqg

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Copper binding site 2 out of 4 in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1352

b:17.9
occ:1.00
NE2 B:HIS68 2.0 16.0 1.0
S2 B:DCD1351 2.2 24.4 1.0
NE2 B:HIS66 2.2 16.9 1.0
NE2 B:HIS112 2.2 12.7 1.0
S1 B:DCD1351 2.9 24.1 1.0
CD2 B:HIS68 3.0 16.8 1.0
C1 B:DCD1351 3.0 23.4 1.0
CE1 B:HIS68 3.1 17.8 1.0
CD2 B:HIS66 3.1 16.1 1.0
CE1 B:HIS112 3.1 13.4 1.0
CE1 B:HIS66 3.2 16.5 1.0
CD2 B:HIS112 3.2 12.0 1.0
CG B:HIS68 4.1 14.7 1.0
ND1 B:HIS68 4.2 16.5 1.0
ND1 B:HIS66 4.2 17.6 1.0
N1 B:DCD1351 4.3 23.3 1.0
ND1 B:HIS112 4.3 12.6 1.0
CG B:HIS66 4.3 15.7 1.0
CG B:HIS112 4.3 12.9 1.0
OE1 B:GLU73 4.5 23.7 1.0
CG B:GLU73 4.5 18.5 1.0
CD B:GLU73 4.6 22.1 1.0
CZ B:PHE132 4.6 25.9 1.0
C2 B:DCD1351 5.0 23.5 1.0

Copper binding site 3 out of 4 in 1gqg

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Copper binding site 3 out of 4 in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1352

b:17.8
occ:1.00
NE2 C:HIS66 2.1 16.6 1.0
NE2 C:HIS68 2.1 16.1 1.0
S1 C:DCD1351 2.1 21.4 1.0
NE2 C:HIS112 2.2 12.2 1.0
S2 C:DCD1351 2.9 23.2 1.0
C1 C:DCD1351 2.9 21.4 1.0
CD2 C:HIS68 3.0 14.9 1.0
CE1 C:HIS66 3.0 16.5 1.0
CE1 C:HIS112 3.1 13.8 1.0
CD2 C:HIS66 3.1 15.5 1.0
CE1 C:HIS68 3.2 17.5 1.0
CD2 C:HIS112 3.2 14.1 1.0
ND1 C:HIS66 4.2 16.8 1.0
CG C:HIS68 4.2 14.8 1.0
ND1 C:HIS112 4.2 12.3 1.0
N1 C:DCD1351 4.2 21.6 1.0
ND1 C:HIS68 4.2 16.9 1.0
CG C:HIS66 4.2 14.7 1.0
CG C:HIS112 4.3 12.6 1.0
OE1 C:GLU73 4.4 22.0 1.0
CG C:GLU73 4.4 18.3 1.0
CD C:GLU73 4.5 20.9 1.0
CZ C:PHE132 4.6 24.7 1.0
C3 C:DCD1351 5.0 21.8 1.0

Copper binding site 4 out of 4 in 1gqg

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Copper binding site 4 out of 4 in the Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Quercetin 2,3-Dioxygenase in Complex with the Inhibitor Diethyldithiocarbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1352

b:17.2
occ:1.00
NE2 D:HIS68 2.1 14.9 1.0
NE2 D:HIS66 2.1 14.9 1.0
NE2 D:HIS112 2.1 13.5 1.0
S2 D:DCD1351 2.3 20.6 1.0
S1 D:DCD1351 2.8 23.7 1.0
C1 D:DCD1351 2.9 21.7 1.0
CD2 D:HIS68 3.0 14.7 1.0
CD2 D:HIS66 3.0 14.1 1.0
CE1 D:HIS112 3.0 15.1 1.0
CE1 D:HIS66 3.1 14.9 1.0
CE1 D:HIS68 3.1 16.6 1.0
CD2 D:HIS112 3.2 13.6 1.0
CG D:HIS68 4.1 14.3 1.0
ND1 D:HIS66 4.2 15.7 1.0
ND1 D:HIS112 4.2 12.9 1.0
CG D:HIS66 4.2 14.4 1.0
ND1 D:HIS68 4.2 15.4 1.0
N1 D:DCD1351 4.2 20.7 1.0
CG D:HIS112 4.3 12.4 1.0
OE1 D:GLU73 4.6 22.7 1.0
CG D:GLU73 4.7 17.3 1.0
CD D:GLU73 4.7 20.0 1.0

Reference:

R.A.Steiner, I.M.Kooter, B.W.Dijkstra. Functional Analysis of the Copper-Dependent Quercetin 2,3-Dioxygenase.1.Ligand-Induced Coordination Changes Probed By X-Ray Crystallography: Inhibition, Ordering Effect and Mechanistic Insights Biochemistry V. 41 7955 2002.
ISSN: ISSN 0006-2960
PubMed: 12069585
DOI: 10.1021/BI0159736
Page generated: Wed Sep 2 21:45:08 2020
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