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Zinc in PDB 1z9p: X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi

Enzymatic activity of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi

All present enzymatic activity of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi:
1.15.1.1;

Protein crystallography data

The structure of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi, PDB code: 1z9p 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) 19.32 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.410, 63.990, 73.970, 90.00, 118.04, 90.00
R / Rfree (%) 17 / 21.2

Other elements in 1z9p:

The structure of X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi (pdb code 1z9p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi, PDB code: 1z9p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1z9p

Go back to Zinc Binding Sites List in 1z9p
Zinc binding site 1 out of 2 in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:16.5
occ:1.00
OD1 A:ASP116 2.0 12.2 1.0
ND1 A:HIS95 2.0 17.2 1.0
ND1 A:HIS113 2.1 15.8 1.0
ND1 A:HIS104 2.1 16.9 1.0
CG A:ASP116 2.8 13.3 1.0
OD2 A:ASP116 2.9 15.2 1.0
CE1 A:HIS95 2.9 20.9 1.0
CE1 A:HIS104 2.9 16.5 1.0
CE1 A:HIS113 3.0 18.4 1.0
CG A:HIS95 3.1 17.8 1.0
CG A:HIS113 3.1 15.3 1.0
CG A:HIS104 3.2 16.9 1.0
CB A:HIS95 3.5 19.1 1.0
CB A:HIS113 3.5 16.2 1.0
CB A:HIS104 3.6 17.9 1.0
CA A:HIS104 3.7 20.1 1.0
NE2 A:HIS95 4.1 20.3 1.0
NE2 A:HIS113 4.1 20.6 1.0
NE2 A:HIS104 4.1 13.9 1.0
CD2 A:HIS95 4.2 22.3 1.0
CB A:ASP116 4.2 12.2 1.0
CD2 A:HIS113 4.2 21.6 1.0
CD2 A:HIS104 4.2 15.8 1.0
CD2 A:LEU164 4.5 25.7 1.0
N A:GLY105 4.6 19.2 1.0
CA A:ASP116 4.7 10.6 1.0
N A:HIS104 4.7 21.7 1.0
C A:HIS104 4.7 20.7 1.0
CA A:HIS113 4.8 14.9 1.0
N A:HIS113 4.8 13.6 1.0
CD2 A:HIS70 4.8 12.4 1.0
N A:ASP116 4.9 11.9 1.0
O A:LYS103 4.9 21.2 1.0
CA A:HIS95 5.0 17.2 1.0

Zinc binding site 2 out of 2 in 1z9p

Go back to Zinc Binding Sites List in 1z9p
Zinc binding site 2 out of 2 in the X-Ray Structure of A Cu-Zn Superoxide Dismutase From Haemophilus Ducreyi


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:13.3
occ:1.00
OD1 B:ASP116 2.0 12.1 1.0
ND1 B:HIS113 2.0 13.7 1.0
ND1 B:HIS95 2.0 13.8 1.0
ND1 B:HIS104 2.1 12.1 1.0
CG B:ASP116 2.8 12.8 1.0
OD2 B:ASP116 2.8 13.4 1.0
CE1 B:HIS104 2.9 11.0 1.0
CE1 B:HIS95 2.9 16.1 1.0
CE1 B:HIS113 3.0 13.6 1.0
CG B:HIS113 3.1 15.0 1.0
CG B:HIS95 3.1 15.2 1.0
CG B:HIS104 3.2 13.6 1.0
CB B:HIS113 3.5 15.4 1.0
CB B:HIS95 3.5 15.2 1.0
CB B:HIS104 3.6 12.9 1.0
CA B:HIS104 3.8 14.1 1.0
NE2 B:HIS104 4.1 9.8 1.0
NE2 B:HIS95 4.1 15.4 1.0
NE2 B:HIS113 4.1 16.0 1.0
CD2 B:HIS113 4.2 14.1 1.0
CD2 B:HIS95 4.2 18.3 1.0
CB B:ASP116 4.2 11.6 1.0
CD2 B:HIS104 4.2 11.3 1.0
CD2 B:LEU164 4.6 17.9 1.0
N B:GLY105 4.7 12.5 1.0
CA B:ASP116 4.7 11.3 1.0
C B:HIS104 4.8 13.7 1.0
N B:HIS104 4.8 14.2 1.0
CD2 B:HIS70 4.8 12.8 1.0
CA B:HIS113 4.8 15.9 1.0
O B:LYS103 4.9 16.6 1.0
N B:HIS113 4.9 16.4 1.0
N B:ASP116 4.9 11.3 1.0
CG B:HIS70 5.0 10.4 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 03:15:26 2020

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