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Iron in PDB 2c1u: Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form

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

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

Protein crystallography data

The structure of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form, PDB code: 2c1u 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) 29.88 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.800, 51.100, 167.900, 90.00, 98.20, 90.00
R / Rfree (%) 16.9 / 22

Other elements in 2c1u:

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

Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form (pdb code 2c1u). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form, PDB code: 2c1u:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 2c1u

Go back to Iron Binding Sites List in 2c1u
Iron binding site 1 out of 8 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised 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 - Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:25.2
occ:1.00
FE A:HEC401 0.0 25.2 1.0
NE2 A:HIS85 2.0 26.6 1.0
ND A:HEC401 2.0 26.4 1.0
NE2 A:HIS69 2.0 25.3 1.0
NC A:HEC401 2.0 25.7 1.0
NB A:HEC401 2.0 26.2 1.0
NA A:HEC401 2.1 24.2 1.0
CE1 A:HIS85 2.9 30.7 1.0
CE1 A:HIS69 3.0 25.1 1.0
C1D A:HEC401 3.0 23.1 1.0
C1B A:HEC401 3.0 26.9 1.0
C4A A:HEC401 3.0 25.5 1.0
C4D A:HEC401 3.0 24.6 1.0
C4C A:HEC401 3.1 25.9 1.0
CD2 A:HIS69 3.1 25.8 1.0
C1A A:HEC401 3.1 26.0 1.0
C1C A:HEC401 3.1 27.9 1.0
CD2 A:HIS85 3.1 27.5 1.0
C4B A:HEC401 3.1 26.7 1.0
CHB A:HEC401 3.3 25.9 1.0
CHD A:HEC401 3.4 25.1 1.0
CHA A:HEC401 3.4 25.3 1.0
CHC A:HEC401 3.4 27.8 1.0
ND1 A:HIS85 4.1 32.7 1.0
ND1 A:HIS69 4.1 21.8 1.0
CG A:HIS85 4.2 31.2 1.0
CG A:HIS69 4.2 25.2 1.0
C2D A:HEC401 4.2 24.6 1.0
C3D A:HEC401 4.2 23.4 1.0
C2B A:HEC401 4.3 27.3 1.0
C3A A:HEC401 4.3 26.6 1.0
C3C A:HEC401 4.3 25.7 1.0
C2C A:HEC401 4.3 25.9 1.0
C2A A:HEC401 4.3 26.5 1.0
C3B A:HEC401 4.3 28.0 1.0

Iron binding site 2 out of 8 in 2c1u

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Iron binding site 2 out of 8 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised 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 - Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:30.4
occ:1.00
FE A:HEC402 0.0 30.4 1.0
NB A:HEC402 2.0 27.4 1.0
NC A:HEC402 2.0 29.6 1.0
NE2 A:HIS215 2.0 26.6 1.0
ND A:HEC402 2.1 27.7 1.0
NA A:HEC402 2.1 27.9 1.0
SD A:MET289 2.3 36.9 1.0
C4B A:HEC402 2.9 29.0 1.0
C1C A:HEC402 3.0 27.4 1.0
CE1 A:HIS215 3.0 28.0 1.0
CD2 A:HIS215 3.0 29.7 1.0
C1D A:HEC402 3.1 26.1 1.0
C4D A:HEC402 3.1 28.2 1.0
C1B A:HEC402 3.1 27.9 1.0
C4C A:HEC402 3.1 29.3 1.0
C1A A:HEC402 3.1 27.5 1.0
C4A A:HEC402 3.1 27.2 1.0
CHC A:HEC402 3.3 28.7 1.0
CHD A:HEC402 3.5 28.5 1.0
CHA A:HEC402 3.5 27.9 1.0
CHB A:HEC402 3.5 29.5 1.0
CG A:MET289 3.5 32.2 1.0
CE A:MET289 3.6 31.2 1.0
ND1 A:HIS215 4.1 29.8 1.0
CG A:HIS215 4.2 29.9 1.0
C3B A:HEC402 4.2 29.6 1.0
C2B A:HEC402 4.2 28.9 1.0
C2C A:HEC402 4.2 29.1 1.0
CB A:MET289 4.3 32.9 1.0
C2D A:HEC402 4.3 28.0 1.0
C3C A:HEC402 4.3 28.5 1.0
C3D A:HEC402 4.3 28.9 1.0
C2A A:HEC402 4.4 26.8 1.0
C3A A:HEC402 4.4 28.1 1.0

Iron binding site 3 out of 8 in 2c1u

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Iron binding site 3 out of 8 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised 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 - Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:26.4
occ:1.00
FE B:HEC401 0.0 26.4 1.0
NB B:HEC401 2.0 25.8 1.0
NE2 B:HIS85 2.0 27.9 1.0
NC B:HEC401 2.0 25.1 1.0
ND B:HEC401 2.0 21.4 1.0
NE2 B:HIS69 2.0 23.1 1.0
NA B:HEC401 2.1 24.9 1.0
CE1 B:HIS85 2.8 29.4 1.0
CD2 B:HIS69 3.0 22.2 1.0
C4B B:HEC401 3.0 24.8 1.0
C1C B:HEC401 3.0 23.8 1.0
C1D B:HEC401 3.0 22.5 1.0
C4D B:HEC401 3.0 25.9 1.0
C1B B:HEC401 3.1 26.2 1.0
CE1 B:HIS69 3.1 20.2 1.0
C4C B:HEC401 3.1 26.2 1.0
C1A B:HEC401 3.1 27.0 1.0
C4A B:HEC401 3.1 26.7 1.0
CD2 B:HIS85 3.2 30.1 1.0
CHC B:HEC401 3.3 23.3 1.0
CHD B:HEC401 3.4 24.1 1.0
CHA B:HEC401 3.4 25.5 1.0
CHB B:HEC401 3.5 27.0 1.0
ND1 B:HIS85 4.0 30.2 1.0
CG B:HIS69 4.1 23.4 1.0
ND1 B:HIS69 4.1 24.8 1.0
CG B:HIS85 4.2 33.0 1.0
C3B B:HEC401 4.2 25.3 1.0
C2B B:HEC401 4.2 26.4 1.0
C2C B:HEC401 4.2 24.0 1.0
C3D B:HEC401 4.3 21.6 1.0
C2D B:HEC401 4.3 22.8 1.0
C3C B:HEC401 4.3 26.7 1.0
C3A B:HEC401 4.4 26.4 1.0
C2A B:HEC401 4.4 27.9 1.0

Iron binding site 4 out of 8 in 2c1u

Go back to Iron Binding Sites List in 2c1u
Iron binding site 4 out of 8 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised 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 - Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:28.1
occ:1.00
FE B:HEC402 0.0 28.1 1.0
NE2 B:HIS215 2.0 25.0 1.0
NA B:HEC402 2.1 28.1 1.0
ND B:HEC402 2.1 29.0 1.0
NB B:HEC402 2.1 28.8 1.0
NC B:HEC402 2.1 27.5 1.0
SD B:MET289 2.4 39.5 1.0
CE1 B:HIS215 3.0 28.9 1.0
CD2 B:HIS215 3.0 27.3 1.0
C1A B:HEC402 3.0 28.6 1.0
C4D B:HEC402 3.1 30.5 1.0
C4A B:HEC402 3.1 27.7 1.0
C1D B:HEC402 3.1 29.4 1.0
C1B B:HEC402 3.1 29.9 1.0
C4B B:HEC402 3.1 30.8 1.0
C1C B:HEC402 3.1 28.9 1.0
C4C B:HEC402 3.1 30.2 1.0
CHB B:HEC402 3.4 30.0 1.0
CHA B:HEC402 3.4 28.9 1.0
CG B:MET289 3.4 35.4 1.0
CHD B:HEC402 3.4 29.6 1.0
CHC B:HEC402 3.5 28.4 1.0
CE B:MET289 3.5 39.9 1.0
ND1 B:HIS215 4.1 25.8 1.0
CG B:HIS215 4.2 31.0 1.0
CB B:MET289 4.2 35.3 1.0
C3D B:HEC402 4.3 30.8 1.0
C3A B:HEC402 4.3 29.4 1.0
C2A B:HEC402 4.3 29.0 1.0
C2D B:HEC402 4.3 29.8 1.0
C2B B:HEC402 4.3 29.7 1.0
C3B B:HEC402 4.3 30.9 1.0
C2C B:HEC402 4.3 27.2 1.0
C3C B:HEC402 4.4 27.6 1.0

Iron binding site 5 out of 8 in 2c1u

Go back to Iron Binding Sites List in 2c1u
Iron binding site 5 out of 8 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:24.1
occ:1.00
FE C:HEC401 0.0 24.1 1.0
NE2 C:HIS85 2.0 24.5 1.0
NC C:HEC401 2.0 21.5 1.0
NB C:HEC401 2.0 25.9 1.0
NE2 C:HIS69 2.0 26.1 1.0
NA C:HEC401 2.1 20.6 1.0
ND C:HEC401 2.1 22.5 1.0
CD2 C:HIS85 3.0 27.5 1.0
CE1 C:HIS85 3.0 26.2 1.0
CE1 C:HIS69 3.0 23.7 1.0
C1B C:HEC401 3.0 23.8 1.0
C1A C:HEC401 3.0 25.1 1.0
C4B C:HEC401 3.0 24.4 1.0
C4D C:HEC401 3.0 23.9 1.0
C1C C:HEC401 3.0 26.9 1.0
C4C C:HEC401 3.0 23.0 1.0
C4A C:HEC401 3.1 23.1 1.0
CD2 C:HIS69 3.1 26.8 1.0
C1D C:HEC401 3.1 23.6 1.0
CHA C:HEC401 3.4 23.4 1.0
CHC C:HEC401 3.4 27.7 1.0
CHB C:HEC401 3.4 24.8 1.0
CHD C:HEC401 3.4 23.4 1.0
ND1 C:HIS85 4.1 28.0 1.0
CG C:HIS85 4.1 31.3 1.0
ND1 C:HIS69 4.1 25.4 1.0
CG C:HIS69 4.2 24.2 1.0
C2B C:HEC401 4.2 24.0 1.0
C2A C:HEC401 4.3 24.6 1.0
C3A C:HEC401 4.3 25.0 1.0
C3B C:HEC401 4.3 26.5 1.0
C2D C:HEC401 4.3 23.8 1.0
C3D C:HEC401 4.3 23.5 1.0
C3C C:HEC401 4.3 20.7 1.0
C2C C:HEC401 4.3 19.7 1.0

Iron binding site 6 out of 8 in 2c1u

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Iron binding site 6 out of 8 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:30.3
occ:1.00
FE C:HEC402 0.0 30.3 1.0
NB C:HEC402 2.0 29.8 1.0
NE2 C:HIS215 2.0 28.6 1.0
NC C:HEC402 2.1 28.6 1.0
NA C:HEC402 2.1 27.6 1.0
ND C:HEC402 2.1 29.4 1.0
SD C:MET289 2.3 36.0 1.0
CE1 C:HIS215 3.0 29.3 1.0
C4B C:HEC402 3.0 29.4 1.0
C1B C:HEC402 3.0 30.7 1.0
C1C C:HEC402 3.0 29.2 1.0
CD2 C:HIS215 3.1 27.6 1.0
C4A C:HEC402 3.1 28.2 1.0
C4D C:HEC402 3.1 30.6 1.0
C1D C:HEC402 3.1 28.8 1.0
C1A C:HEC402 3.1 31.4 1.0
C4C C:HEC402 3.1 29.5 1.0
CE C:MET289 3.3 33.5 1.0
CHC C:HEC402 3.4 28.9 1.0
CG C:MET289 3.4 33.9 1.0
CHB C:HEC402 3.4 28.4 1.0
CHA C:HEC402 3.5 29.7 1.0
CHD C:HEC402 3.5 28.9 1.0
ND1 C:HIS215 4.1 30.5 1.0
CG C:HIS215 4.2 29.8 1.0
C3B C:HEC402 4.2 28.1 1.0
C2B C:HEC402 4.2 29.4 1.0
CB C:MET289 4.3 31.5 1.0
C2C C:HEC402 4.3 28.5 1.0
C2D C:HEC402 4.3 28.5 1.0
C3A C:HEC402 4.3 30.1 1.0
C3D C:HEC402 4.3 29.5 1.0
C2A C:HEC402 4.3 28.8 1.0
C3C C:HEC402 4.4 30.2 1.0

Iron binding site 7 out of 8 in 2c1u

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Iron binding site 7 out of 8 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:25.2
occ:1.00
FE D:HEC401 0.0 25.2 1.0
NE2 D:HIS85 2.0 23.5 1.0
NC D:HEC401 2.0 25.8 1.0
NA D:HEC401 2.0 24.7 1.0
NE2 D:HIS69 2.0 23.2 1.0
NB D:HEC401 2.1 24.4 1.0
ND D:HEC401 2.1 23.4 1.0
C1C D:HEC401 3.0 23.9 1.0
CE1 D:HIS85 3.0 26.0 1.0
CD2 D:HIS85 3.0 26.6 1.0
CD2 D:HIS69 3.0 24.0 1.0
C4A D:HEC401 3.0 25.8 1.0
C4B D:HEC401 3.0 23.3 1.0
CE1 D:HIS69 3.0 23.0 1.0
C1D D:HEC401 3.1 24.9 1.0
C1B D:HEC401 3.1 24.8 1.0
C1A D:HEC401 3.1 27.8 1.0
C4C D:HEC401 3.1 27.3 1.0
C4D D:HEC401 3.1 27.7 1.0
CHC D:HEC401 3.3 24.3 1.0
CHB D:HEC401 3.4 27.5 1.0
CHD D:HEC401 3.4 25.5 1.0
CHA D:HEC401 3.5 26.2 1.0
ND1 D:HIS85 4.1 25.7 1.0
CG D:HIS85 4.1 32.1 1.0
ND1 D:HIS69 4.2 26.5 1.0
CG D:HIS69 4.2 23.5 1.0
C2C D:HEC401 4.2 25.9 1.0
C3A D:HEC401 4.3 29.6 1.0
C2D D:HEC401 4.3 26.4 1.0
C2B D:HEC401 4.3 26.3 1.0
C2A D:HEC401 4.3 29.5 1.0
C3C D:HEC401 4.3 24.0 1.0
C3B D:HEC401 4.3 23.9 1.0
C3D D:HEC401 4.3 23.6 1.0

Iron binding site 8 out of 8 in 2c1u

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Iron binding site 8 out of 8 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Paracoccus Pantotrophus - Oxidised Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe402

b:29.7
occ:1.00
FE D:HEC402 0.0 29.7 1.0
NB D:HEC402 2.0 30.1 1.0
NE2 D:HIS215 2.0 30.0 1.0
ND D:HEC402 2.1 29.8 1.0
NA D:HEC402 2.1 29.6 1.0
NC D:HEC402 2.1 29.5 1.0
SD D:MET289 2.3 36.8 1.0
C4B D:HEC402 3.0 29.9 1.0
CE1 D:HIS215 3.0 29.9 1.0
CD2 D:HIS215 3.0 30.3 1.0
C1B D:HEC402 3.0 28.9 1.0
C1A D:HEC402 3.0 29.8 1.0
C4D D:HEC402 3.1 32.2 1.0
C1C D:HEC402 3.1 30.7 1.0
C1D D:HEC402 3.1 31.2 1.0
C4A D:HEC402 3.1 28.6 1.0
C4C D:HEC402 3.1 29.6 1.0
CHC D:HEC402 3.4 30.8 1.0
CHA D:HEC402 3.4 29.4 1.0
CHB D:HEC402 3.5 30.1 1.0
CHD D:HEC402 3.5 30.0 1.0
CG D:MET289 3.5 34.8 1.0
CE D:MET289 3.5 38.5 1.0
ND1 D:HIS215 4.1 30.1 1.0
CG D:HIS215 4.2 29.5 1.0
C3B D:HEC402 4.2 29.6 1.0
C2B D:HEC402 4.2 30.3 1.0
CB D:MET289 4.3 34.9 1.0
C2A D:HEC402 4.3 27.5 1.0
C2C D:HEC402 4.3 30.0 1.0
C3D D:HEC402 4.3 31.3 1.0
C2D D:HEC402 4.3 31.1 1.0
C3A D:HEC402 4.3 29.9 1.0
C3C D:HEC402 4.3 30.3 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 19:53:48 2024

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