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Iron in PDB 2vhd: Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Pseudomonas Aeruginosa - Mixed Valence Form

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

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

Protein crystallography data

The structure of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Pseudomonas Aeruginosa - Mixed Valence Form, PDB code: 2vhd was solved by A.Echalier, T.Brittain, J.Wright, S.Boycheva, G.B.Mortuza, V.Fulop, N.J.Watmough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.70 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.200, 44.800, 106.200, 90.00, 106.70, 90.00
R / Rfree (%) 18.4 / 24.6

Other elements in 2vhd:

The structure of Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Pseudomonas Aeruginosa - 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 Pseudomonas Aeruginosa - Mixed Valence Form (pdb code 2vhd). 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 Pseudomonas Aeruginosa - Mixed Valence Form, PDB code: 2vhd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2vhd

Go back to Iron Binding Sites List in 2vhd
Iron binding site 1 out of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Pseudomonas Aeruginosa - 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 Pseudomonas Aeruginosa - Mixed Valence Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:38.7
occ:1.00
 FE A:HEC401 0.0 38.7 1.0
ND A:HEC401 2.0 37.4 1.0
NB A:HEC401 2.0 38.0 1.0
NC A:HEC401 2.0 37.4 1.0
NA A:HEC401 2.1 37.7 1.0
NE2 A:HIS55 2.1 32.9 1.0
O A:HOH2053 2.9 42.6 1.0
C4D A:HEC401 3.0 37.2 1.0
C1B A:HEC401 3.0 38.5 1.0
C4B A:HEC401 3.1 36.7 1.0
C1D A:HEC401 3.1 36.0 1.0
C1A A:HEC401 3.1 35.3 1.0
C1C A:HEC401 3.1 37.2 1.0
C4C A:HEC401 3.1 38.6 1.0
C4A A:HEC401 3.1 36.5 1.0
CD2 A:HIS55 3.1 33.7 1.0
CE1 A:HIS55 3.1 36.4 1.0
CHA A:HEC401 3.4 34.2 1.0
CHB A:HEC401 3.4 36.1 1.0
CHC A:HEC401 3.4 36.3 1.0
CHD A:HEC401 3.4 36.6 1.0
NE2 A:GLN104 4.0 39.5 1.0
ND1 A:HIS55 4.2 34.9 1.0
CG A:HIS55 4.2 34.4 1.0
C2B A:HEC401 4.2 37.8 1.0
C3B A:HEC401 4.3 36.5 1.0
C3D A:HEC401 4.3 36.6 1.0
C2D A:HEC401 4.3 34.5 1.0
C2A A:HEC401 4.3 35.1 1.0
C3A A:HEC401 4.3 37.8 1.0
C2C A:HEC401 4.3 38.4 1.0
C3C A:HEC401 4.3 37.7 1.0
CG A:PRO108 4.5 41.2 1.0
CB A:PRO108 4.7 40.3 1.0
CD A:GLN104 5.0 41.0 1.0
OE1 A:GLU114 5.0 50.9 1.0

Iron binding site 2 out of 4 in 2vhd

Go back to Iron Binding Sites List in 2vhd
Iron binding site 2 out of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Pseudomonas Aeruginosa - 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 Pseudomonas Aeruginosa - Mixed Valence Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:44.0
occ:1.00
 FE A:HEC402 0.0 44.0 1.0
ND A:HEC402 2.0 45.1 1.0
NE2 A:HIS201 2.0 43.2 1.0
NB A:HEC402 2.1 44.8 1.0
NC A:HEC402 2.1 45.0 1.0
NA A:HEC402 2.1 45.1 1.0
SD A:MET275 2.3 53.5 1.0
CE1 A:HIS201 2.9 46.0 1.0
C1D A:HEC402 3.0 45.1 1.0
C4D A:HEC402 3.0 44.8 1.0
C4C A:HEC402 3.1 45.5 1.0
C4B A:HEC402 3.1 45.5 1.0
C1B A:HEC402 3.1 45.2 1.0
C1A A:HEC402 3.1 44.4 1.0
C4A A:HEC402 3.1 44.8 1.0
C1C A:HEC402 3.1 44.1 1.0
CD2 A:HIS201 3.2 43.1 1.0
CHD A:HEC402 3.4 45.2 1.0
CHA A:HEC402 3.4 44.5 1.0
CHB A:HEC402 3.5 44.7 1.0
CG A:MET275 3.5 49.7 1.0
CHC A:HEC402 3.5 43.9 1.0
CE A:MET275 3.7 53.1 1.0
ND1 A:HIS201 4.1 46.2 1.0
C2D A:HEC402 4.2 44.8 1.0
C3D A:HEC402 4.2 44.1 1.0
CG A:HIS201 4.2 45.3 1.0
CB A:MET275 4.3 48.3 1.0
C2B A:HEC402 4.3 45.4 1.0
C3C A:HEC402 4.3 44.8 1.0
C3B A:HEC402 4.3 45.9 1.0
C2C A:HEC402 4.3 45.9 1.0
C3A A:HEC402 4.4 43.5 1.0
C2A A:HEC402 4.4 42.9 1.0
CG A:GLN279 5.0 47.1 1.0

Iron binding site 3 out of 4 in 2vhd

Go back to Iron Binding Sites List in 2vhd
Iron binding site 3 out of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Pseudomonas Aeruginosa - 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 Pseudomonas Aeruginosa - Mixed Valence Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:38.0
occ:1.00
 FE B:HEC401 0.0 38.0 1.0
NA B:HEC401 2.0 36.6 1.0
ND B:HEC401 2.0 35.9 1.0
NC B:HEC401 2.0 36.1 1.0
NB B:HEC401 2.0 37.5 1.0
NE2 B:HIS55 2.0 34.8 1.0
O B:HOH2142 2.6 30.7 1.0
C4D B:HEC401 3.0 36.5 1.0
C1A B:HEC401 3.0 35.4 1.0
C4B B:HEC401 3.0 34.0 1.0
C1C B:HEC401 3.0 36.1 1.0
CE1 B:HIS55 3.0 34.1 1.0
C1D B:HEC401 3.0 36.1 1.0
CD2 B:HIS55 3.0 31.7 1.0
C4A B:HEC401 3.1 34.9 1.0
C1B B:HEC401 3.1 35.9 1.0
C4C B:HEC401 3.1 35.2 1.0
CHA B:HEC401 3.3 35.4 1.0
CHC B:HEC401 3.3 34.3 1.0
CHD B:HEC401 3.4 35.0 1.0
CHB B:HEC401 3.5 35.0 1.0
NE2 B:GLN104 4.0 36.4 1.0
ND1 B:HIS55 4.1 31.3 1.0
CG B:HIS55 4.2 32.3 1.0
C3D B:HEC401 4.2 35.7 1.0
C2A B:HEC401 4.2 35.2 1.0
C3B B:HEC401 4.2 33.2 1.0
C2D B:HEC401 4.2 33.1 1.0
C2C B:HEC401 4.2 34.4 1.0
C2B B:HEC401 4.3 35.6 1.0
C3A B:HEC401 4.3 31.8 1.0
C3C B:HEC401 4.3 34.1 1.0
CG B:PRO108 4.5 38.7 1.0
CB B:PRO108 4.5 38.2 1.0
OE1 B:GLU114 4.9 40.5 1.0
CD B:GLN104 5.0 37.4 1.0

Iron binding site 4 out of 4 in 2vhd

Go back to Iron Binding Sites List in 2vhd
Iron binding site 4 out of 4 in the Crystal Structure of the Di-Haem Cytochrome C Peroxidase From Pseudomonas Aeruginosa - 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 Pseudomonas Aeruginosa - Mixed Valence Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:40.6
occ:1.00
 FE B:HEC402 0.0 40.6 1.0
ND B:HEC402 2.0 39.2 1.0
NE2 B:HIS201 2.0 43.6 1.0
NA B:HEC402 2.0 38.1 1.0
NB B:HEC402 2.1 38.9 1.0
NC B:HEC402 2.1 39.9 1.0
SD B:MET275 2.4 43.1 1.0
CE1 B:HIS201 2.9 40.9 1.0
C4D B:HEC402 3.0 39.4 1.0
C1D B:HEC402 3.0 41.0 1.0
C4A B:HEC402 3.0 37.9 1.0
CD2 B:HIS201 3.0 41.9 1.0
C1A B:HEC402 3.1 37.5 1.0
C1B B:HEC402 3.1 38.9 1.0
C4C B:HEC402 3.1 40.2 1.0
C1C B:HEC402 3.2 39.4 1.0
C4B B:HEC402 3.2 38.9 1.0
CG B:MET275 3.3 43.1 1.0
CHD B:HEC402 3.4 39.8 1.0
CHA B:HEC402 3.4 38.2 1.0
CHB B:HEC402 3.4 38.1 1.0
CHC B:HEC402 3.5 38.1 1.0
CE B:MET275 3.9 39.0 1.0
ND1 B:HIS201 4.0 40.3 1.0
CG B:HIS201 4.1 40.3 1.0
C3D B:HEC402 4.2 39.4 1.0
C2D B:HEC402 4.2 39.4 1.0
CB B:MET275 4.3 41.7 1.0
C3A B:HEC402 4.3 35.8 1.0
C2A B:HEC402 4.3 36.1 1.0
C2B B:HEC402 4.3 39.0 1.0
C3C B:HEC402 4.3 39.3 1.0
C2C B:HEC402 4.4 38.9 1.0
C3B B:HEC402 4.4 38.0 1.0
CG B:GLN279 5.0 44.9 1.0

Reference:

A.Echalier, T.Brittain, J.Wright, S.Boycheva, G.B.Mortuza, V.Fulop, N.J.Watmough. Redox-Linked Structural Changes Associated with the Formation of A Catalytically Competent Form of the Diheme Cytochrome C Peroxidase From Pseudomonas Aeruginosa Biochemistry V. 47 1947 2008.
ISSN: ISSN 0006-2960
PubMed: 18217775
DOI: 10.1021/BI702064F
Page generated: Sun Aug 4 02:38:40 2024

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