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Copper in PDB 1z9n: X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface

Enzymatic activity of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface

All present enzymatic activity of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface:
1.15.1.1;

Protein crystallography data

The structure of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface, PDB code: 1z9n was solved by K.Djinovic Carugo, I.Toeroe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.50 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.320, 65.900, 69.540, 66.59, 89.87, 76.03
R / Rfree (%) 15.7 / 19.3

Other elements in 1z9n:

The structure of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface (pdb code 1z9n). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface, PDB code: 1z9n:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1z9n

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Copper binding site 1 out of 4 in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu200

b:17.0
occ:1.00
NE2 A:HIS72 2.0 14.1 1.0
NE2 A:HIS151 2.0 11.9 1.0
ND1 A:HIS70 2.0 10.7 1.0
CE1 A:HIS72 2.9 16.8 1.0
CE1 A:HIS70 2.9 14.5 1.0
CD2 A:HIS151 3.0 12.6 1.0
CE1 A:HIS151 3.0 13.7 1.0
CD2 A:HIS72 3.0 12.4 1.0
CG A:HIS70 3.0 11.3 1.0
NE2 A:HIS95 3.2 14.3 1.0
O A:HOH1122 3.3 31.0 1.0
CB A:HIS70 3.4 10.2 1.0
CD2 A:HIS95 3.6 14.9 1.0
CB A:MET149 3.9 13.1 1.0
CG A:MET149 3.9 13.4 1.0
CE1 A:HIS95 4.0 12.2 1.0
ND1 A:HIS72 4.0 13.5 1.0
NE2 A:HIS70 4.1 11.9 1.0
ND1 A:HIS151 4.1 15.1 1.0
CG A:HIS151 4.1 12.3 1.0
CG A:HIS72 4.1 12.5 1.0
CD2 A:HIS70 4.1 11.4 1.0
O A:HOH1037 4.2 20.8 1.0
N A:HIS70 4.4 9.4 1.0
CA A:HIS70 4.4 11.0 1.0
CG A:HIS95 4.6 12.8 1.0
O A:HIS70 4.6 11.7 1.0
ND1 A:HIS95 4.7 12.2 1.0
C A:HIS70 4.7 10.5 1.0
O A:MET149 4.8 11.7 1.0

Copper binding site 2 out of 4 in 1z9n

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Copper binding site 2 out of 4 in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu200

b:14.0
occ:1.00
ND1 B:HIS70 2.0 10.6 1.0
NE2 B:HIS72 2.0 10.3 1.0
NE2 B:HIS151 2.0 11.5 1.0
CE1 B:HIS70 2.9 10.6 1.0
CE1 B:HIS72 3.0 11.8 1.0
CD2 B:HIS151 3.0 9.3 1.0
CD2 B:HIS72 3.0 10.2 1.0
CG B:HIS70 3.0 9.8 1.0
CE1 B:HIS151 3.1 9.9 1.0
NE2 B:HIS95 3.2 14.6 1.0
CB B:HIS70 3.3 8.8 1.0
O B:HOH240 3.5 20.1 1.0
CD2 B:HIS95 3.6 15.5 1.0
CB B:MET149 3.9 10.8 1.0
CG B:MET149 3.9 11.5 1.0
CE1 B:HIS95 4.0 16.8 1.0
NE2 B:HIS70 4.1 9.6 1.0
ND1 B:HIS72 4.1 10.3 1.0
CD2 B:HIS70 4.1 10.4 1.0
CG B:HIS151 4.1 10.5 1.0
CG B:HIS72 4.1 11.0 1.0
ND1 B:HIS151 4.2 11.4 1.0
O B:HOH223 4.3 17.4 1.0
CA B:HIS70 4.4 7.7 1.0
N B:HIS70 4.4 7.4 1.0
CG B:HIS95 4.5 11.8 1.0
O B:HIS70 4.6 8.0 1.0
ND1 B:HIS95 4.7 11.8 1.0
C B:HIS70 4.8 7.7 1.0
O B:MET149 4.8 10.0 1.0

Copper binding site 3 out of 4 in 1z9n

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Copper binding site 3 out of 4 in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu200

b:15.1
occ:1.00
NE2 C:HIS72 2.0 11.3 1.0
ND1 C:HIS70 2.0 11.0 1.0
NE2 C:HIS151 2.0 10.9 1.0
CE1 C:HIS72 2.9 10.8 1.0
CE1 C:HIS70 3.0 12.5 1.0
CD2 C:HIS151 3.0 10.0 1.0
CD2 C:HIS72 3.0 11.2 1.0
CG C:HIS70 3.0 9.7 1.0
CE1 C:HIS151 3.0 11.0 1.0
NE2 C:HIS95 3.2 13.9 1.0
O C:HOH2038 3.3 21.1 1.0
CB C:HIS70 3.4 9.8 1.0
CD2 C:HIS95 3.6 14.1 1.0
CB C:MET149 3.9 10.6 1.0
CG C:MET149 3.9 12.2 1.0
CE1 C:HIS95 4.0 14.7 1.0
ND1 C:HIS72 4.1 11.5 1.0
NE2 C:HIS70 4.1 9.2 1.0
CG C:HIS72 4.1 12.1 1.0
CG C:HIS151 4.1 10.9 1.0
CD2 C:HIS70 4.1 10.3 1.0
ND1 C:HIS151 4.1 12.1 1.0
O C:HOH2034 4.3 18.7 1.0
CA C:HIS70 4.4 8.0 1.0
N C:HIS70 4.4 8.1 1.0
CG C:HIS95 4.5 13.2 1.0
O C:HIS70 4.6 10.3 1.0
ND1 C:HIS95 4.7 12.9 1.0
C C:HIS70 4.8 8.9 1.0
O C:MET149 4.9 10.1 1.0

Copper binding site 4 out of 4 in 1z9n

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Copper binding site 4 out of 4 in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi with Haem Bound at the Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu200

b:22.2
occ:1.00
NE2 D:HIS72 2.0 18.3 1.0
ND1 D:HIS70 2.0 13.5 1.0
NE2 D:HIS151 2.0 19.0 1.0
CD2 D:HIS151 2.9 12.0 1.0
CE1 D:HIS72 2.9 14.8 1.0
CE1 D:HIS70 2.9 14.7 1.0
CD2 D:HIS72 3.0 18.5 1.0
O D:HOH319 3.0 33.6 1.0
CG D:HIS70 3.0 15.2 1.0
CE1 D:HIS151 3.1 15.1 1.0
NE2 D:HIS95 3.2 17.9 1.0
CB D:HIS70 3.4 14.6 1.0
CD2 D:HIS95 3.7 16.2 1.0
CB D:MET149 3.9 15.5 1.0
CG D:MET149 3.9 14.2 1.0
CE1 D:HIS95 4.0 13.3 1.0
ND1 D:HIS72 4.1 18.4 1.0
NE2 D:HIS70 4.1 13.7 1.0
CG D:HIS151 4.1 16.5 1.0
CG D:HIS72 4.1 19.3 1.0
CD2 D:HIS70 4.1 15.1 1.0
ND1 D:HIS151 4.2 17.9 1.0
N D:HIS70 4.4 13.0 1.0
CA D:HIS70 4.4 13.1 1.0
O D:HOH251 4.4 24.1 1.0
CG D:HIS95 4.6 14.7 1.0
O D:HIS70 4.7 13.8 1.0
ND1 D:HIS95 4.8 10.9 1.0
O D:MET149 4.8 15.3 1.0
C D:HIS70 4.8 12.0 1.0
O D:HOH309 4.9 31.7 1.0

Reference:

I.Toro, C.Petrutz, F.Pacello, M.D'orazio, A.Battistoni, K.Djinovic-Carugo. Structural Basis of Heme Binding in the Cu,Zn Superoxide Dismutase From Haemophilus Ducreyi. J.Mol.Biol. V. 386 406 2009.
ISSN: ISSN 0022-2836
PubMed: 19103206
DOI: 10.1016/J.JMB.2008.12.004
Page generated: Wed Oct 28 14:18:20 2020
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