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Zinc 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
Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1z9n

Go back to Zinc Binding Sites List in 1z9n
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:12.0
occ:1.00
OD1 A:ASP116 2.0 10.7 1.0
ND1 A:HIS95 2.1 12.2 1.0
ND1 A:HIS113 2.1 11.5 1.0
ND1 A:HIS104 2.1 10.0 1.0
CG A:ASP116 2.7 11.1 1.0
OD2 A:ASP116 2.8 11.6 1.0
CE1 A:HIS104 2.9 10.0 1.0
CE1 A:HIS113 3.0 14.0 1.0
CE1 A:HIS95 3.0 12.2 1.0
CG A:HIS95 3.1 12.8 1.0
CG A:HIS113 3.1 12.3 1.0
CG A:HIS104 3.2 10.3 1.0
CB A:HIS95 3.5 14.4 1.0
CB A:HIS113 3.5 10.7 1.0
CB A:HIS104 3.6 10.4 1.0
CA A:HIS104 3.8 12.6 1.0
NE2 A:HIS104 4.1 10.6 1.0
NE2 A:HIS113 4.1 14.1 1.0
NE2 A:HIS95 4.1 14.3 1.0
CB A:ASP116 4.2 9.8 1.0
CD2 A:HIS95 4.2 14.9 1.0
CD2 A:HIS113 4.2 14.2 1.0
CD2 A:HIS104 4.3 11.0 1.0
CD2 A:LEU164 4.4 15.2 1.0
CA A:ASP116 4.7 9.9 1.0
N A:GLY105 4.7 12.4 1.0
CA A:HIS113 4.8 12.8 1.0
N A:HIS104 4.8 12.4 1.0
C A:HIS104 4.8 13.2 1.0
CD2 A:HIS70 4.8 11.4 1.0
N A:HIS113 4.8 13.4 1.0
N A:ASP116 4.8 11.0 1.0
CG A:HIS70 4.9 11.3 1.0

Zinc binding site 2 out of 4 in 1z9n

Go back to Zinc Binding Sites List in 1z9n
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:10.8
occ:1.00
OD1 B:ASP116 2.0 9.2 1.0
ND1 B:HIS104 2.0 9.9 1.0
ND1 B:HIS113 2.1 11.1 1.0
ND1 B:HIS95 2.1 11.8 1.0
CG B:ASP116 2.7 8.1 1.0
OD2 B:ASP116 2.8 10.7 1.0
CE1 B:HIS104 2.9 9.8 1.0
CE1 B:HIS95 3.0 16.8 1.0
CE1 B:HIS113 3.0 12.1 1.0
CG B:HIS113 3.1 11.8 1.0
CG B:HIS95 3.1 11.8 1.0
CG B:HIS104 3.2 10.7 1.0
CB B:HIS113 3.5 11.3 1.0
CB B:HIS95 3.5 12.1 1.0
CB B:HIS104 3.6 11.2 1.0
CA B:HIS104 3.8 11.8 1.0
NE2 B:HIS104 4.1 10.3 1.0
NE2 B:HIS95 4.1 14.6 1.0
NE2 B:HIS113 4.1 12.5 1.0
CB B:ASP116 4.2 9.3 1.0
CD2 B:HIS95 4.2 15.5 1.0
CD2 B:HIS113 4.2 11.8 1.0
CD2 B:HIS104 4.2 11.1 1.0
CD2 B:LEU164 4.6 18.6 1.0
N B:GLY105 4.7 9.6 1.0
CA B:ASP116 4.7 8.9 1.0
CA B:HIS113 4.7 10.7 1.0
C B:HIS104 4.8 12.2 1.0
N B:HIS104 4.8 11.2 1.0
N B:HIS113 4.8 11.2 1.0
CD2 B:HIS70 4.9 10.4 1.0
N B:ASP116 4.9 9.1 1.0
O B:LYS103 4.9 11.8 1.0

Zinc binding site 3 out of 4 in 1z9n

Go back to Zinc Binding Sites List in 1z9n
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:11.2
occ:1.00
OD1 C:ASP116 2.0 9.2 1.0
ND1 C:HIS95 2.1 12.9 1.0
ND1 C:HIS113 2.1 13.2 1.0
ND1 C:HIS104 2.1 9.4 1.0
CG C:ASP116 2.7 9.5 1.0
OD2 C:ASP116 2.8 10.5 1.0
CE1 C:HIS104 2.9 10.2 1.0
CE1 C:HIS95 2.9 14.7 1.0
CE1 C:HIS113 2.9 13.8 1.0
CG C:HIS113 3.1 14.2 1.0
CG C:HIS95 3.1 13.2 1.0
CG C:HIS104 3.2 10.0 1.0
CB C:HIS113 3.5 11.6 1.0
CB C:HIS95 3.6 14.6 1.0
CB C:HIS104 3.6 11.3 1.0
CA C:HIS104 3.8 12.4 1.0
NE2 C:HIS95 4.1 13.9 1.0
NE2 C:HIS104 4.1 9.9 1.0
NE2 C:HIS113 4.1 12.2 1.0
CB C:ASP116 4.2 8.9 1.0
CD2 C:HIS95 4.2 14.1 1.0
CD2 C:HIS113 4.2 13.0 1.0
CD2 C:HIS104 4.2 9.4 1.0
CD2 C:LEU164 4.6 17.3 1.0
CA C:ASP116 4.7 9.1 1.0
N C:GLY105 4.7 11.0 1.0
CA C:HIS113 4.7 12.2 1.0
N C:HIS104 4.7 12.1 1.0
C C:HIS104 4.8 12.5 1.0
N C:HIS113 4.8 12.9 1.0
CD2 C:HIS70 4.8 10.3 1.0
N C:ASP116 4.9 9.7 1.0
O C:LYS103 4.9 14.9 1.0

Zinc binding site 4 out of 4 in 1z9n

Go back to Zinc Binding Sites List in 1z9n
Zinc 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 Zinc with other atoms in the Zn 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:Zn201

b:13.7
occ:1.00
OD1 D:ASP116 2.0 11.6 1.0
ND1 D:HIS95 2.0 10.9 1.0
ND1 D:HIS113 2.1 13.2 1.0
ND1 D:HIS104 2.1 12.7 1.0
CG D:ASP116 2.7 9.1 1.0
OD2 D:ASP116 2.8 12.9 1.0
CE1 D:HIS104 2.9 13.0 1.0
CE1 D:HIS95 2.9 13.3 1.0
CE1 D:HIS113 3.0 17.1 1.0
CG D:HIS113 3.1 12.8 1.0
CG D:HIS95 3.1 14.7 1.0
CG D:HIS104 3.2 11.3 1.0
CB D:HIS113 3.5 13.3 1.0
CB D:HIS95 3.5 17.1 1.0
CB D:HIS104 3.6 11.7 1.0
CA D:HIS104 3.8 12.0 1.0
NE2 D:HIS95 4.1 17.9 1.0
NE2 D:HIS104 4.1 11.1 1.0
NE2 D:HIS113 4.1 15.6 1.0
CB D:ASP116 4.2 12.4 1.0
CD2 D:HIS95 4.2 16.2 1.0
CD2 D:HIS113 4.2 15.7 1.0
CD2 D:HIS104 4.2 12.9 1.0
CD2 D:LEU164 4.5 15.0 1.0
CA D:ASP116 4.7 11.8 1.0
N D:GLY105 4.7 13.3 1.0
CA D:HIS113 4.7 13.8 1.0
N D:HIS104 4.8 12.9 1.0
CD2 D:HIS70 4.8 15.1 1.0
C D:HIS104 4.8 13.5 1.0
N D:HIS113 4.8 15.6 1.0
N D:ASP116 4.9 13.4 1.0
CG D:HIS70 5.0 15.2 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 Dec 16 03:15:27 2020

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