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Iron in PDB 2c1v: Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form

Enzymatic activity of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form

All present enzymatic activity of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form:
1.11.1.5;

Protein crystallography data

The structure of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form, PDB code: 2c1v was solved by A.Echalier, V.Fulop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.22 / 1.2
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.370, 141.200, 51.580, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 18.8

Other elements in 2c1v:

The structure of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form (pdb code 2c1v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form, PDB code: 2c1v:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2c1v

Go back to Iron Binding Sites List in 2c1v
Iron binding site 1 out of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:9.6
occ:1.00
 FE A:HEC401 0.0 9.6 1.0
NC A:HEC401 2.0 9.7 1.0
NA A:HEC401 2.0 9.8 1.0
ND A:HEC401 2.0 10.2 1.0
NB A:HEC401 2.0 9.8 1.0
NE2 A:HIS69 2.0 10.3 1.0
O A:HOH2498 2.1 17.3 1.0
C1D A:HEC401 3.0 10.1 1.0
C4A A:HEC401 3.0 9.8 1.0
CE1 A:HIS69 3.0 10.5 1.0
C4C A:HEC401 3.0 9.8 1.0
CD2 A:HIS69 3.0 10.1 1.0
C1B A:HEC401 3.0 9.6 1.0
C4D A:HEC401 3.0 9.5 1.0
C1A A:HEC401 3.0 8.9 1.0
C4B A:HEC401 3.0 9.6 1.0
C1C A:HEC401 3.0 10.0 1.0
CHD A:HEC401 3.4 10.6 1.0
CHB A:HEC401 3.4 10.1 1.0
CHA A:HEC401 3.4 9.2 1.0
CHC A:HEC401 3.4 10.0 1.0
NE2 A:GLN118 4.0 11.4 1.0
ND1 A:HIS69 4.1 10.4 1.0
CG A:HIS69 4.2 10.5 1.0
C2D A:HEC401 4.2 9.7 1.0
C3A A:HEC401 4.2 9.9 1.0
C3C A:HEC401 4.2 10.1 1.0
C2B A:HEC401 4.2 9.7 1.0
C2A A:HEC401 4.2 9.9 1.0
O A:HOH2255 4.2 21.2 1.0
C3D A:HEC401 4.2 10.6 1.0
C2C A:HEC401 4.3 10.0 1.0
C3B A:HEC401 4.3 9.4 1.0
OE1 A:GLU128 4.6 21.9 1.0
CG A:PRO122 4.7 14.3 1.0
CB A:PRO122 4.7 12.8 1.0

Iron binding site 2 out of 4 in 2c1v

Go back to Iron Binding Sites List in 2c1v
Iron binding site 2 out of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:10.5
occ:1.00
 FE A:HEC402 0.0 10.5 1.0
NA A:HEC402 2.0 10.3 1.0
NB A:HEC402 2.0 10.5 1.0
ND A:HEC402 2.0 10.0 1.0
NC A:HEC402 2.0 11.3 1.0
NE2 A:HIS215 2.1 11.0 1.0
SD A:MET289 2.3 13.4 1.0
C1A A:HEC402 3.0 10.1 1.0
CE1 A:HIS215 3.0 10.7 1.0
C1D A:HEC402 3.0 10.7 1.0
C4D A:HEC402 3.0 9.6 1.0
C4B A:HEC402 3.0 11.3 1.0
C1B A:HEC402 3.0 11.2 1.0
C4A A:HEC402 3.1 10.6 1.0
C4C A:HEC402 3.1 10.8 1.0
CD2 A:HIS215 3.1 10.8 1.0
C1C A:HEC402 3.1 10.4 1.0
CHB A:HEC402 3.4 11.3 1.0
CHA A:HEC402 3.4 10.5 1.0
CHC A:HEC402 3.4 11.9 1.0
CHD A:HEC402 3.4 11.1 1.0
CG A:MET289 3.4 13.2 1.0
CE A:MET289 3.4 12.7 1.0
ND1 A:HIS215 4.2 10.5 1.0
CG A:HIS215 4.2 11.3 1.0
CB A:MET289 4.2 12.7 1.0
C3B A:HEC402 4.2 11.9 1.0
C3D A:HEC402 4.3 11.2 1.0
C2D A:HEC402 4.3 11.1 1.0
C2A A:HEC402 4.3 10.2 1.0
C2B A:HEC402 4.3 11.8 1.0
C3A A:HEC402 4.3 11.5 1.0
C2C A:HEC402 4.3 10.7 1.0
C3C A:HEC402 4.3 11.5 1.0
CG A:GLN293 5.0 13.2 1.0

Iron binding site 3 out of 4 in 2c1v

Go back to Iron Binding Sites List in 2c1v
Iron binding site 3 out of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:9.4
occ:1.00
 FE B:HEC401 0.0 9.4 1.0
NB B:HEC401 2.0 8.8 1.0
ND B:HEC401 2.0 9.9 1.0
NA B:HEC401 2.0 8.9 1.0
NC B:HEC401 2.0 8.4 1.0
NE2 B:HIS69 2.1 9.3 1.0
O B:HOH2537 2.1 17.9 1.0
C1D B:HEC401 3.0 10.5 1.0
C1B B:HEC401 3.0 9.7 1.0
C4A B:HEC401 3.0 9.5 1.0
C4C B:HEC401 3.0 9.8 1.0
CE1 B:HIS69 3.0 10.0 1.0
C4D B:HEC401 3.1 9.7 1.0
C1A B:HEC401 3.1 10.0 1.0
C4B B:HEC401 3.1 9.3 1.0
CD2 B:HIS69 3.1 9.1 1.0
C1C B:HEC401 3.1 8.9 1.0
CHD B:HEC401 3.3 11.1 1.0
CHB B:HEC401 3.3 10.3 1.0
CHC B:HEC401 3.4 9.4 1.0
CHA B:HEC401 3.4 9.5 1.0
NE2 B:GLN118 4.0 12.5 1.0
ND1 B:HIS69 4.2 10.6 1.0
CG B:HIS69 4.2 9.5 1.0
O B:HOH2285 4.2 20.4 1.0
C3C B:HEC401 4.2 9.8 1.0
C2A B:HEC401 4.2 10.6 1.0
C3A B:HEC401 4.3 10.1 1.0
C2B B:HEC401 4.3 10.2 1.0
C2D B:HEC401 4.3 10.3 1.0
C3D B:HEC401 4.3 10.2 1.0
C3B B:HEC401 4.3 8.9 1.0
C2C B:HEC401 4.3 8.9 1.0
CG B:PRO122 4.7 14.2 1.0
CB B:PRO122 4.7 12.4 1.0

Iron binding site 4 out of 4 in 2c1v

Go back to Iron Binding Sites List in 2c1v
Iron binding site 4 out of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Mixed Valence Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:12.9
occ:1.00
 FE B:HEC402 0.0 12.9 1.0
NB B:HEC402 2.0 12.7 1.0
ND B:HEC402 2.0 12.5 1.0
NA B:HEC402 2.0 12.5 1.0
NC B:HEC402 2.0 13.4 1.0
NE2 B:HIS215 2.1 13.6 1.0
SD B:MET289 2.3 15.8 1.0
C4B B:HEC402 3.0 12.6 1.0
CE1 B:HIS215 3.0 13.1 1.0
C1D B:HEC402 3.0 13.1 1.0
C4D B:HEC402 3.0 11.5 1.0
C1B B:HEC402 3.0 13.6 1.0
CD2 B:HIS215 3.1 13.5 1.0
C1C B:HEC402 3.1 13.1 1.0
C4A B:HEC402 3.1 13.7 1.0
C4C B:HEC402 3.1 13.4 1.0
C1A B:HEC402 3.1 13.3 1.0
CHC B:HEC402 3.4 13.4 1.0
CHA B:HEC402 3.4 12.3 1.0
CHB B:HEC402 3.4 14.0 1.0
CHD B:HEC402 3.4 13.7 1.0
CG B:MET289 3.4 16.2 1.0
CE B:MET289 3.5 15.1 1.0
ND1 B:HIS215 4.2 13.6 1.0
CB B:MET289 4.2 14.4 1.0
CG B:HIS215 4.2 13.7 1.0
C3D B:HEC402 4.3 13.5 1.0
C3B B:HEC402 4.3 16.2 1.0
C2D B:HEC402 4.3 12.8 1.0
C3C B:HEC402 4.3 14.0 1.0
C2B B:HEC402 4.3 14.3 1.0
C2C B:HEC402 4.3 13.3 1.0
C2A B:HEC402 4.3 13.6 1.0
C3A B:HEC402 4.3 15.0 1.0
CG B:GLN293 5.0 15.1 1.0

Reference:

A.Echalier, C.F.Goodhew, G.W.Pettigrew, V.Fulop. Activation and Catalysis of the Di-Heme Cytochrome C Peroxidase From Paracoccus Pantotrophus Structure V. 14 107 2006.
ISSN: ISSN 0969-2126
PubMed: 16407070
DOI: 10.1016/J.STR.2005.09.011
Page generated: Sat Aug 3 19:54:57 2024

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