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Iron 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:

Copper (Cu) 4 atoms
Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron 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 Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 1z9n

Go back to Iron Binding Sites List in 1z9n
Iron binding site 1 out of 2 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 Iron with other atoms in the Fe 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:Fe1001

b:15.1
occ:1.00
FE A:HEM1001 0.0 15.1 1.0
NA A:HEM1001 2.0 16.0 1.0
NE2 A:HIS64 2.0 14.6 1.0
NE2 B:HIS124 2.0 11.4 1.0
NB A:HEM1001 2.0 13.1 1.0
NC A:HEM1001 2.0 14.9 1.0
ND A:HEM1001 2.1 16.8 1.0
CE1 B:HIS124 2.9 11.8 1.0
CE1 A:HIS64 3.0 12.8 1.0
CD2 A:HIS64 3.0 12.8 1.0
C4B A:HEM1001 3.0 12.1 1.0
C1C A:HEM1001 3.0 15.9 1.0
C4C A:HEM1001 3.0 18.3 1.0
C4A A:HEM1001 3.0 17.1 1.0
C1B A:HEM1001 3.0 13.6 1.0
CD2 B:HIS124 3.0 11.8 1.0
C4D A:HEM1001 3.0 17.9 1.0
C1A A:HEM1001 3.0 19.0 1.0
C1D A:HEM1001 3.1 18.8 1.0
CHC A:HEM1001 3.4 15.6 1.0
CHD A:HEM1001 3.4 17.9 1.0
CHA A:HEM1001 3.4 20.0 1.0
CHB A:HEM1001 3.4 16.1 1.0
ND1 B:HIS124 4.1 11.8 1.0
ND1 A:HIS64 4.1 13.1 1.0
CG A:HIS64 4.1 13.9 1.0
CG B:HIS124 4.2 10.5 1.0
C3C A:HEM1001 4.2 19.9 1.0
C2C A:HEM1001 4.2 20.8 1.0
C3B A:HEM1001 4.2 13.3 1.0
C2B A:HEM1001 4.2 15.0 1.0
C3A A:HEM1001 4.3 20.1 1.0
C2A A:HEM1001 4.3 22.5 1.0
C3D A:HEM1001 4.3 25.6 1.0
C2D A:HEM1001 4.3 19.9 1.0

Iron binding site 2 out of 2 in 1z9n

Go back to Iron Binding Sites List in 1z9n
Iron binding site 2 out of 2 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 Iron with other atoms in the Fe 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
C:Fe2001

b:12.8
occ:1.00
FE C:HEM2001 0.0 12.8 1.0
NE2 C:HIS124 1.9 11.9 1.0
NE2 D:HIS64 2.0 12.1 1.0
NC C:HEM2001 2.0 12.8 1.0
NA C:HEM2001 2.0 14.4 1.0
NB C:HEM2001 2.1 10.2 1.0
ND C:HEM2001 2.1 12.4 1.0
CE1 C:HIS124 2.9 9.9 1.0
CD2 D:HIS64 3.0 13.6 1.0
CE1 D:HIS64 3.0 12.0 1.0
CD2 C:HIS124 3.0 11.2 1.0
C4B C:HEM2001 3.0 11.3 1.0
C4A C:HEM2001 3.0 13.6 1.0
C1C C:HEM2001 3.0 12.1 1.0
C1B C:HEM2001 3.0 11.8 1.0
C4C C:HEM2001 3.0 15.0 1.0
C1D C:HEM2001 3.1 16.6 1.0
C4D C:HEM2001 3.1 14.1 1.0
C1A C:HEM2001 3.1 14.8 1.0
CHC C:HEM2001 3.4 12.9 1.0
CHB C:HEM2001 3.4 14.7 1.0
CHD C:HEM2001 3.4 13.5 1.0
CHA C:HEM2001 3.5 16.1 1.0
ND1 C:HIS124 4.1 10.1 1.0
ND1 D:HIS64 4.1 12.4 1.0
CG D:HIS64 4.1 14.5 1.0
CG C:HIS124 4.1 10.6 1.0
C3B C:HEM2001 4.2 11.0 1.0
C2C C:HEM2001 4.2 14.0 1.0
C2B C:HEM2001 4.3 12.6 1.0
C3A C:HEM2001 4.3 16.5 1.0
C3C C:HEM2001 4.3 15.1 1.0
C2A C:HEM2001 4.3 16.8 1.0
C2D C:HEM2001 4.3 16.5 1.0
C3D C:HEM2001 4.3 14.0 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 14:38:48 2020

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