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Iron in PDB 1zzh: Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus

Enzymatic activity of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus

All present enzymatic activity of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus:
1.11.1.5;

Protein crystallography data

The structure of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus, PDB code: 1zzh was solved by L.De Smet, S.N.Savvides, E.Van Horen, G.Pettigrew, J.J.Vanbeeumen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.630, 132.470, 163.940, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 27.8

Other elements in 1zzh:

The structure of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Zinc (Zn) 8 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus (pdb code 1zzh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus, PDB code: 1zzh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1zzh

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Iron binding site 1 out of 8 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe802

b:44.0
occ:1.00
 FE A:HEC802 0.0 44.0 1.0
NA A:HEC802 1.9 46.1 1.0
NB A:HEC802 1.9 45.4 1.0
ND A:HEC802 2.0 47.6 1.0
NC A:HEC802 2.0 45.5 1.0
NE2 A:HIS58 2.0 32.1 1.0
NE2 A:HIS74 2.3 44.8 1.0
C4A A:HEC802 3.0 46.9 1.0
C4B A:HEC802 3.0 44.8 1.0
C1A A:HEC802 3.0 48.3 1.0
C1B A:HEC802 3.0 45.3 1.0
CE1 A:HIS58 3.0 35.5 1.0
C4D A:HEC802 3.0 49.1 1.0
C1C A:HEC802 3.0 45.3 1.0
C4C A:HEC802 3.0 46.4 1.0
C1D A:HEC802 3.0 48.8 1.0
CD2 A:HIS58 3.0 33.9 1.0
CD2 A:HIS74 3.1 47.6 1.0
CE1 A:HIS74 3.3 48.0 1.0
CHB A:HEC802 3.4 45.5 1.0
CHA A:HEC802 3.4 50.0 1.0
CHC A:HEC802 3.4 45.2 1.0
CHD A:HEC802 3.4 48.2 1.0
ND1 A:HIS58 4.1 36.7 1.0
CG A:HIS58 4.2 35.5 1.0
C3B A:HEC802 4.2 45.0 1.0
C3A A:HEC802 4.2 49.7 1.0
C2B A:HEC802 4.3 44.3 1.0
C2A A:HEC802 4.3 49.4 1.0
C3D A:HEC802 4.3 50.3 1.0
C3C A:HEC802 4.3 47.4 1.0
C2C A:HEC802 4.3 45.9 1.0
C2D A:HEC802 4.3 49.8 1.0
CG A:HIS74 4.3 49.9 1.0
ND1 A:HIS74 4.4 49.8 1.0

Iron binding site 2 out of 8 in 1zzh

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Iron binding site 2 out of 8 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe803

b:42.8
occ:1.00
 FE A:HEC803 0.0 42.8 1.0
NB A:HEC803 1.9 41.7 1.0
NA A:HEC803 2.0 42.7 1.0
NC A:HEC803 2.0 45.6 1.0
ND A:HEC803 2.0 43.2 1.0
NE2 A:HIS204 2.2 39.9 1.0
SD A:MET278 2.5 46.0 1.0
C4B A:HEC803 3.0 44.5 1.0
C4A A:HEC803 3.0 43.0 1.0
C1B A:HEC803 3.0 41.9 1.0
C1A A:HEC803 3.0 43.8 1.0
C4D A:HEC803 3.0 44.4 1.0
C1C A:HEC803 3.0 47.1 1.0
C4C A:HEC803 3.0 46.4 1.0
C1D A:HEC803 3.0 44.0 1.0
CD2 A:HIS204 3.1 42.9 1.0
CE1 A:HIS204 3.2 39.5 1.0
CHB A:HEC803 3.4 43.1 1.0
CHC A:HEC803 3.4 46.9 1.0
CHA A:HEC803 3.4 45.0 1.0
CHD A:HEC803 3.4 45.8 1.0
CG A:MET278 3.4 46.5 1.0
CE A:MET278 4.1 44.3 1.0
CG A:HIS204 4.2 44.6 1.0
C3B A:HEC803 4.2 43.6 1.0
C3A A:HEC803 4.2 44.2 1.0
C2B A:HEC803 4.2 42.0 1.0
ND1 A:HIS204 4.2 43.1 1.0
C2A A:HEC803 4.3 44.5 1.0
C3D A:HEC803 4.3 44.9 1.0
C3C A:HEC803 4.3 48.5 1.0
C2C A:HEC803 4.3 47.2 1.0
C2D A:HEC803 4.3 44.4 1.0
CB A:MET278 4.6 46.4 1.0

Iron binding site 3 out of 8 in 1zzh

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Iron binding site 3 out of 8 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:32.9
occ:1.00
 FE B:HEC401 0.0 32.9 1.0
NB B:HEC401 1.9 33.2 1.0
NA B:HEC401 1.9 34.1 1.0
ND B:HEC401 2.0 34.7 1.0
NC B:HEC401 2.0 34.0 1.0
NE2 B:HIS58 2.1 28.7 1.0
NE2 B:HIS74 2.2 38.8 1.0
C4A B:HEC401 3.0 36.5 1.0
C4B B:HEC401 3.0 34.2 1.0
C4D B:HEC401 3.0 37.7 1.0
C1A B:HEC401 3.0 35.2 1.0
C4C B:HEC401 3.0 35.7 1.0
C1D B:HEC401 3.0 35.5 1.0
C1B B:HEC401 3.0 32.5 1.0
C1C B:HEC401 3.0 33.1 1.0
CE1 B:HIS58 3.1 28.2 1.0
CD2 B:HIS74 3.1 38.9 1.0
CD2 B:HIS58 3.1 28.9 1.0
CE1 B:HIS74 3.3 41.3 1.0
CHB B:HEC401 3.4 34.1 1.0
CHA B:HEC401 3.4 37.0 1.0
CHC B:HEC401 3.4 33.1 1.0
CHD B:HEC401 3.4 33.9 1.0
ND1 B:HIS58 4.2 30.7 1.0
C3B B:HEC401 4.2 35.1 1.0
CG B:HIS58 4.2 29.6 1.0
C3A B:HEC401 4.2 37.4 1.0
C2B B:HEC401 4.3 34.0 1.0
C3D B:HEC401 4.3 37.8 1.0
C2A B:HEC401 4.3 36.3 1.0
C3C B:HEC401 4.3 36.6 1.0
C2D B:HEC401 4.3 36.9 1.0
CG B:HIS74 4.3 41.2 1.0
C2C B:HEC401 4.3 34.1 1.0
ND1 B:HIS74 4.3 41.6 1.0

Iron binding site 4 out of 8 in 1zzh

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Iron binding site 4 out of 8 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:38.9
occ:1.00
 FE B:HEC402 0.0 38.9 1.0
NB B:HEC402 1.9 40.7 1.0
NA B:HEC402 2.0 42.6 1.0
NC B:HEC402 2.0 42.5 1.0
ND B:HEC402 2.0 40.7 1.0
NE2 B:HIS204 2.2 42.5 1.0
SD B:MET278 2.4 36.6 1.0
C4B B:HEC402 3.0 41.9 1.0
C1B B:HEC402 3.0 41.4 1.0
C1C B:HEC402 3.0 43.3 1.0
C4A B:HEC402 3.0 43.5 1.0
C4C B:HEC402 3.0 43.7 1.0
C1A B:HEC402 3.0 43.1 1.0
C4D B:HEC402 3.0 41.0 1.0
C1D B:HEC402 3.0 41.7 1.0
CD2 B:HIS204 3.1 41.5 1.0
CE1 B:HIS204 3.2 41.9 1.0
CHC B:HEC402 3.4 42.1 1.0
CHB B:HEC402 3.4 42.8 1.0
CG B:MET278 3.4 39.6 1.0
CHA B:HEC402 3.4 42.4 1.0
CHD B:HEC402 3.4 42.5 1.0
CE B:MET278 4.0 34.8 1.0
C3B B:HEC402 4.2 41.5 1.0
C2B B:HEC402 4.2 40.4 1.0
C3C B:HEC402 4.3 44.9 1.0
C2C B:HEC402 4.3 44.2 1.0
C3A B:HEC402 4.3 44.4 1.0
C3D B:HEC402 4.3 40.0 1.0
C2A B:HEC402 4.3 44.2 1.0
CG B:HIS204 4.3 42.3 1.0
ND1 B:HIS204 4.3 42.9 1.0
C2D B:HEC402 4.3 41.4 1.0
CB B:MET278 4.5 41.9 1.0

Iron binding site 5 out of 8 in 1zzh

Go back to Iron Binding Sites List in 1zzh
Iron binding site 5 out of 8 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:35.1
occ:1.00
 FE C:HEC401 0.0 35.1 1.0
NB C:HEC401 1.9 38.1 1.0
NA C:HEC401 2.0 40.0 1.0
NC C:HEC401 2.0 38.2 1.0
ND C:HEC401 2.0 41.1 1.0
NE2 C:HIS58 2.1 29.2 1.0
NE2 C:HIS74 2.2 38.1 1.0
C4B C:HEC401 3.0 39.0 1.0
C4A C:HEC401 3.0 39.4 1.0
C1C C:HEC401 3.0 38.1 1.0
C4C C:HEC401 3.0 39.8 1.0
C1B C:HEC401 3.0 37.2 1.0
C1A C:HEC401 3.0 38.7 1.0
C4D C:HEC401 3.0 43.7 1.0
C1D C:HEC401 3.0 40.8 1.0
CD2 C:HIS74 3.1 38.9 1.0
CD2 C:HIS58 3.1 30.4 1.0
CE1 C:HIS58 3.1 28.7 1.0
CE1 C:HIS74 3.3 41.1 1.0
CHC C:HEC401 3.4 39.4 1.0
CHB C:HEC401 3.4 36.9 1.0
CHD C:HEC401 3.4 39.4 1.0
CHA C:HEC401 3.4 41.2 1.0
ND1 C:HIS58 4.2 29.6 1.0
CG C:HIS58 4.2 30.6 1.0
C3B C:HEC401 4.2 37.5 1.0
C3A C:HEC401 4.2 40.6 1.0
C3C C:HEC401 4.3 41.4 1.0
C2B C:HEC401 4.3 37.5 1.0
C2C C:HEC401 4.3 38.5 1.0
C2A C:HEC401 4.3 39.1 1.0
C3D C:HEC401 4.3 44.3 1.0
CG C:HIS74 4.3 41.6 1.0
C2D C:HEC401 4.3 42.9 1.0
ND1 C:HIS74 4.3 42.9 1.0

Iron binding site 6 out of 8 in 1zzh

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Iron binding site 6 out of 8 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:36.6
occ:1.00
 FE C:HEC402 0.0 36.6 1.0
NB C:HEC402 1.9 39.1 1.0
NA C:HEC402 2.0 37.1 1.0
ND C:HEC402 2.0 35.7 1.0
NC C:HEC402 2.0 39.5 1.0
NE2 C:HIS204 2.2 42.3 1.0
SD C:MET278 2.3 39.1 1.0
C4B C:HEC402 3.0 40.9 1.0
C4A C:HEC402 3.0 36.9 1.0
C1B C:HEC402 3.0 40.3 1.0
C1A C:HEC402 3.0 37.0 1.0
C4D C:HEC402 3.0 37.7 1.0
C4C C:HEC402 3.0 40.4 1.0
C1D C:HEC402 3.0 37.1 1.0
C1C C:HEC402 3.0 40.4 1.0
CD2 C:HIS204 3.1 42.5 1.0
CE1 C:HIS204 3.2 42.8 1.0
CHB C:HEC402 3.4 38.9 1.0
CHA C:HEC402 3.4 37.1 1.0
CHC C:HEC402 3.4 38.8 1.0
CHD C:HEC402 3.4 39.4 1.0
CG C:MET278 3.4 39.1 1.0
CE C:MET278 4.0 39.8 1.0
C3B C:HEC402 4.2 42.0 1.0
C3D C:HEC402 4.3 37.8 1.0
C3A C:HEC402 4.3 37.0 1.0
CG C:HIS204 4.3 43.6 1.0
C2B C:HEC402 4.3 41.8 1.0
C2A C:HEC402 4.3 36.8 1.0
C3C C:HEC402 4.3 42.2 1.0
ND1 C:HIS204 4.3 43.2 1.0
C2D C:HEC402 4.3 36.9 1.0
C2C C:HEC402 4.3 40.9 1.0
CB C:MET278 4.6 40.3 1.0

Iron binding site 7 out of 8 in 1zzh

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Iron binding site 7 out of 8 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:38.0
occ:1.00
 FE D:HEC401 0.0 38.0 1.0
NB D:HEC401 1.9 38.3 1.0
NA D:HEC401 1.9 39.8 1.0
ND D:HEC401 2.0 41.0 1.0
NC D:HEC401 2.0 38.8 1.0
NE2 D:HIS58 2.0 35.9 1.0
NE2 D:HIS74 2.2 40.9 1.0
C4B D:HEC401 3.0 40.3 1.0
C4A D:HEC401 3.0 41.9 1.0
C1A D:HEC401 3.0 41.6 1.0
C1B D:HEC401 3.0 38.0 1.0
C4D D:HEC401 3.0 42.4 1.0
CE1 D:HIS58 3.0 36.5 1.0
C4C D:HEC401 3.0 40.1 1.0
C1C D:HEC401 3.0 41.1 1.0
C1D D:HEC401 3.0 42.5 1.0
CD2 D:HIS58 3.0 34.5 1.0
CD2 D:HIS74 3.1 42.9 1.0
CE1 D:HIS74 3.3 43.1 1.0
CHB D:HEC401 3.4 40.3 1.0
CHC D:HEC401 3.4 42.5 1.0
CHA D:HEC401 3.4 42.5 1.0
CHD D:HEC401 3.4 42.8 1.0
ND1 D:HIS58 4.1 37.0 1.0
CG D:HIS58 4.2 36.5 1.0
C3B D:HEC401 4.2 38.9 1.0
C3A D:HEC401 4.2 43.1 1.0
C2B D:HEC401 4.3 38.7 1.0
C3C D:HEC401 4.3 40.7 1.0
C3D D:HEC401 4.3 43.4 1.0
C2A D:HEC401 4.3 43.5 1.0
C2C D:HEC401 4.3 41.5 1.0
C2D D:HEC401 4.3 42.4 1.0
CG D:HIS74 4.3 46.4 1.0
ND1 D:HIS74 4.4 44.6 1.0

Iron binding site 8 out of 8 in 1zzh

Go back to Iron Binding Sites List in 1zzh
Iron binding site 8 out of 8 in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:38.0
occ:1.00
 FE D:HEC402 0.0 38.0 1.0
NA D:HEC402 1.9 36.4 1.0
NB D:HEC402 1.9 35.8 1.0
ND D:HEC402 2.0 36.5 1.0
NC D:HEC402 2.0 40.4 1.0
NE2 D:HIS204 2.2 42.2 1.0
SD D:MET278 2.4 46.0 1.0
C1A D:HEC402 3.0 37.2 1.0
C4A D:HEC402 3.0 36.9 1.0
C4B D:HEC402 3.0 34.8 1.0
C4D D:HEC402 3.0 38.0 1.0
C1B D:HEC402 3.0 36.1 1.0
C1C D:HEC402 3.0 41.5 1.0
C4C D:HEC402 3.0 41.5 1.0
C1D D:HEC402 3.0 39.5 1.0
CD2 D:HIS204 3.1 42.7 1.0
CE1 D:HIS204 3.2 42.7 1.0
CHA D:HEC402 3.4 36.5 1.0
CHB D:HEC402 3.4 36.7 1.0
CHC D:HEC402 3.4 38.1 1.0
CHD D:HEC402 3.4 40.3 1.0
CG D:MET278 3.5 45.9 1.0
CE D:MET278 4.0 50.4 1.0
CG D:HIS204 4.2 43.2 1.0
ND1 D:HIS204 4.2 40.6 1.0
C3A D:HEC402 4.2 37.0 1.0
C3B D:HEC402 4.2 38.0 1.0
C2A D:HEC402 4.2 37.3 1.0
C3D D:HEC402 4.2 40.4 1.0
C2B D:HEC402 4.3 36.5 1.0
C3C D:HEC402 4.3 44.1 1.0
C2C D:HEC402 4.3 43.8 1.0
C2D D:HEC402 4.3 40.9 1.0
CB D:MET278 4.6 42.5 1.0

Reference:

L.De Smet, S.N.Savvides, E.Van Horen, G.Pettigrew, J.J.Van Beeumen. Structural and Mutagenesis Studies on the Cytochrome C Peroxidase From Rhodobacter Capsulatus Provide New Insights Into Structure-Function Relationships of Bacterial Di-Heme Peroxidases J.Biol.Chem. V. 281 4371 2006.
ISSN: ISSN 0021-9258
PubMed: 16314410
DOI: 10.1074/JBC.M509582200
Page generated: Sun Dec 13 14:39:10 2020

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