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Zinc 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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of the Fully Oxidized Di-Heme Cytochrome C Peroxidase From R. Capsulatus, PDB code: 1zzh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1zzh

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Zinc 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 Zinc with other atoms in the Zn 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:Zn402

b:67.3
occ:1.00
NE2 A:HIS264 2.4 45.8 1.0
CD2 A:HIS264 3.1 42.6 1.0
CE1 A:HIS264 3.6 44.6 1.0
CG A:HIS264 4.4 42.4 1.0
CB A:SER265 4.5 40.6 1.0
ND1 A:HIS264 4.6 42.2 1.0

Zinc binding site 2 out of 8 in 1zzh

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:44.9
occ:1.00
OD2 A:ASP293 2.0 36.7 1.0
OD1 A:ASP289 2.3 55.5 1.0
OD2 A:ASP289 2.5 57.8 1.0
CG A:ASP289 2.7 55.0 1.0
CG A:ASP293 2.9 38.6 1.0
OD1 A:ASP293 3.1 42.9 1.0
NH1 A:ARG272 3.3 68.1 1.0
NH2 A:ARG272 3.5 63.4 1.0
CZ A:ARG272 3.9 65.5 1.0
O A:ASP289 3.9 55.2 1.0
CB A:ASP289 4.1 53.2 1.0
C A:ASP289 4.3 52.3 1.0
CB A:ASP293 4.4 39.6 1.0
CA A:ASP289 4.7 51.9 1.0

Zinc binding site 3 out of 8 in 1zzh

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Zinc 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 Zinc with other atoms in the Zn 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:Zn502

b:83.9
occ:1.00
NE2 B:HIS264 2.3 40.8 1.0
CD2 B:HIS264 3.0 39.0 1.0
CE1 B:HIS264 3.4 39.4 1.0
CG B:HIS264 4.2 36.9 1.0
CB B:SER265 4.3 31.1 1.0
ND1 B:HIS264 4.4 38.5 1.0
O B:VAL219 4.9 40.2 1.0
CA B:SER265 5.0 31.5 1.0

Zinc binding site 4 out of 8 in 1zzh

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Zinc 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 Zinc with other atoms in the Zn 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:Zn503

b:74.2
occ:1.00
OE2 B:GLU163 1.9 32.0 1.0
OE1 B:GLU160 2.7 58.6 1.0
CD B:GLU163 3.0 36.0 1.0
OE1 B:GLU163 3.4 39.8 1.0
CMA B:HEC401 3.4 33.8 1.0
CD B:GLU160 3.5 55.3 1.0
OE2 B:GLU160 3.6 60.4 1.0
CG B:GLU163 4.3 33.9 1.0
CHB B:HEC401 4.6 34.1 1.0
C3A B:HEC401 4.6 37.4 1.0
CMB B:HEC401 4.6 35.6 1.0
CG1 B:VAL159 4.9 30.4 1.0
CG B:GLU160 5.0 51.3 1.0

Zinc binding site 5 out of 8 in 1zzh

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Zinc 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 Zinc with other atoms in the Zn 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
B:Zn504

b:66.3
occ:1.00
OD1 B:ASP244 2.3 58.4 1.0
CG B:ASP244 3.2 57.3 1.0
OE2 B:GLU245 3.2 69.3 1.0
OD1 B:ASP243 3.2 64.9 1.0
OD2 B:ASP244 3.3 54.0 1.0
CG B:ASP243 4.0 64.0 1.0
OD2 B:ASP243 4.1 63.6 1.0
CD B:GLU245 4.3 68.7 1.0
N B:ASP244 4.6 59.3 1.0
CB B:ASP244 4.6 58.8 1.0
CG B:GLU245 4.8 66.2 1.0

Zinc binding site 6 out of 8 in 1zzh

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Zinc 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 Zinc with other atoms in the Zn 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
B:Zn802

b:52.3
occ:1.00
OD2 B:ASP293 1.9 48.5 1.0
OD1 B:ASP289 2.7 61.0 1.0
CG B:ASP293 2.9 48.0 1.0
OD1 B:ASP293 3.2 51.4 1.0
OD2 B:ASP289 3.4 66.2 1.0
CG B:ASP289 3.5 62.4 1.0
NH1 B:ARG272 4.0 50.5 1.0
CB B:ASP293 4.2 44.6 1.0
O B:ASP289 4.4 57.6 1.0
NH2 B:ARG272 4.6 51.9 1.0
C B:ASP289 4.8 58.0 1.0
CZ B:ARG272 4.8 50.5 1.0
CB B:ASP289 4.9 59.8 1.0

Zinc binding site 7 out of 8 in 1zzh

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Zinc 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 Zinc with other atoms in the Zn 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
C:Zn602

b:72.3
occ:1.00
NE2 C:HIS264 2.4 40.6 1.0
CD2 C:HIS264 3.2 38.8 1.0
CE1 C:HIS264 3.5 39.5 1.0
CG C:HIS264 4.4 39.2 1.0
ND1 C:HIS264 4.6 41.0 1.0
CB C:SER265 4.6 34.6 1.0
O C:VAL219 5.0 39.4 1.0

Zinc binding site 8 out of 8 in 1zzh

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Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:83.7
occ:1.00
NE2 D:HIS264 2.4 41.2 1.0
CD2 D:HIS264 3.2 41.0 1.0
CE1 D:HIS264 3.4 41.2 1.0
CG D:HIS264 4.4 40.9 1.0
ND1 D:HIS264 4.5 41.7 1.0
CB D:SER265 4.6 39.1 1.0
O D:VAL219 4.7 41.7 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: Sat Sep 26 00:46:37 2020
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