Atomistry » Copper » PDB 1x9r-2ahl » 1z9n
Atomistry »
  Copper »
    PDB 1x9r-2ahl »
      1z9n »

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

Go back to Copper Binding Sites List in 1z9n
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

Go back to Copper Binding Sites List in 1z9n
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

Go back to Copper Binding Sites List in 1z9n
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

Go back to Copper Binding Sites List in 1z9n
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: Sun Dec 13 11:03:16 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy