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Iron in PDB 6qkn: Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae

Enzymatic activity of Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae

All present enzymatic activity of Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae:
1.11.1.5;

Protein crystallography data

The structure of Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae, PDB code: 6qkn was solved by A.L.Carvalho, M.J.Romao, S.Pauleta, C.Nobrega, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.95 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.120, 89.140, 94.830, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 23.3

Other elements in 6qkn:

The structure of Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae (pdb code 6qkn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae, PDB code: 6qkn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6qkn

Go back to Iron Binding Sites List in 6qkn
Iron binding site 1 out of 4 in the Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae


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 Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:24.2
occ:1.00
FE A:HEC401 0.0 24.2 1.0
NA A:HEC401 2.0 24.5 1.0
NE2 A:HIS59 2.0 22.8 1.0
NB A:HEC401 2.1 21.1 1.0
NC A:HEC401 2.1 22.1 1.0
ND A:HEC401 2.2 26.6 1.0
N3 A:AZI404 2.3 30.0 1.0
N2 A:AZI404 2.9 46.0 1.0
CD2 A:HIS59 2.9 21.0 1.0
C4A A:HEC401 3.0 23.7 1.0
C1A A:HEC401 3.0 24.9 1.0
C1B A:HEC401 3.0 20.5 1.0
CE1 A:HIS59 3.0 22.4 1.0
C4D A:HEC401 3.1 26.1 1.0
C4B A:HEC401 3.1 20.8 1.0
C4C A:HEC401 3.1 24.6 1.0
C1C A:HEC401 3.1 21.9 1.0
C1D A:HEC401 3.2 27.6 1.0
CHB A:HEC401 3.2 21.1 1.0
CHA A:HEC401 3.3 26.2 1.0
CHC A:HEC401 3.5 19.8 1.0
CHD A:HEC401 3.5 27.2 1.0
N1 A:AZI404 3.8 43.4 1.0
NE2 A:GLN108 4.0 28.3 1.0
CG A:HIS59 4.1 22.6 1.0
ND1 A:HIS59 4.1 20.5 1.0
C2A A:HEC401 4.3 25.3 1.0
C3A A:HEC401 4.3 24.1 1.0
C3B A:HEC401 4.3 20.3 1.0
C2B A:HEC401 4.4 22.0 1.0
C3C A:HEC401 4.4 22.7 1.0
C3D A:HEC401 4.4 28.0 1.0
C2C A:HEC401 4.4 21.4 1.0
C2D A:HEC401 4.5 28.8 1.0
CG A:PRO112 4.7 24.5 1.0
CB A:PRO112 4.8 24.0 1.0
CD A:GLN108 4.9 29.1 1.0

Iron binding site 2 out of 4 in 6qkn

Go back to Iron Binding Sites List in 6qkn
Iron binding site 2 out of 4 in the Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae


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 Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:36.7
occ:1.00
FE A:HEC402 0.0 36.7 1.0
ND A:HEC402 2.1 34.6 1.0
NC A:HEC402 2.2 44.7 1.0
NB A:HEC402 2.2 37.5 1.0
NA A:HEC402 2.2 31.6 1.0
NE2 A:HIS204 2.2 31.6 1.0
SD A:MET280 2.4 45.6 1.0
C1D A:HEC402 3.1 34.5 1.0
C4D A:HEC402 3.1 32.9 1.0
C4C A:HEC402 3.1 43.1 1.0
C4B A:HEC402 3.1 39.0 1.0
C1B A:HEC402 3.1 38.2 1.0
CD2 A:HIS204 3.2 33.2 1.0
C1A A:HEC402 3.2 33.3 1.0
C1C A:HEC402 3.2 41.4 1.0
C4A A:HEC402 3.2 33.2 1.0
CE1 A:HIS204 3.3 34.3 1.0
CHD A:HEC402 3.4 42.9 1.0
CHA A:HEC402 3.4 33.1 1.0
CHB A:HEC402 3.5 35.9 1.0
CHC A:HEC402 3.5 39.6 1.0
CG A:MET280 3.5 49.6 1.0
CE A:MET280 3.7 43.1 1.0
CG A:HIS204 4.3 34.1 1.0
C3B A:HEC402 4.3 40.8 1.0
ND1 A:HIS204 4.4 33.8 1.0
C2B A:HEC402 4.4 38.9 1.0
C3C A:HEC402 4.4 46.8 1.0
C2D A:HEC402 4.4 32.6 1.0
C3D A:HEC402 4.4 31.0 1.0
CB A:MET280 4.4 43.5 1.0
C2C A:HEC402 4.5 44.8 1.0
C2A A:HEC402 4.5 33.5 1.0
C3A A:HEC402 4.5 34.4 1.0
CG A:GLN284 5.0 43.5 1.0

Iron binding site 3 out of 4 in 6qkn

Go back to Iron Binding Sites List in 6qkn
Iron binding site 3 out of 4 in the Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae


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 Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:21.9
occ:1.00
FE B:HEC401 0.0 21.9 1.0
NC B:HEC401 1.9 18.9 1.0
NE2 B:HIS59 2.0 18.4 1.0
ND B:HEC401 2.1 25.4 1.0
NA B:HEC401 2.1 19.2 1.0
NB B:HEC401 2.2 22.9 1.0
N1 B:AZI404 2.5 38.2 1.0
C4C B:HEC401 2.9 20.6 1.0
CD2 B:HIS59 2.9 17.7 1.0
C1C B:HEC401 3.0 20.2 1.0
C1D B:HEC401 3.0 23.8 1.0
CE1 B:HIS59 3.1 18.9 1.0
N2 B:AZI404 3.1 55.8 1.0
C1A B:HEC401 3.1 21.2 1.0
C4D B:HEC401 3.1 23.5 1.0
C4A B:HEC401 3.1 20.5 1.0
C4B B:HEC401 3.1 22.4 1.0
C1B B:HEC401 3.1 22.1 1.0
CHD B:HEC401 3.3 20.9 1.0
CHA B:HEC401 3.4 22.2 1.0
CHC B:HEC401 3.4 20.6 1.0
CHB B:HEC401 3.4 20.3 1.0
N3 B:AZI404 4.0 59.9 1.0
NE2 B:GLN108 4.1 20.4 1.0
CG B:HIS59 4.1 18.1 1.0
ND1 B:HIS59 4.1 20.0 1.0
C3C B:HEC401 4.2 20.7 1.0
C2C B:HEC401 4.3 19.4 1.0
C2D B:HEC401 4.4 24.8 1.0
C3B B:HEC401 4.4 22.2 1.0
C3D B:HEC401 4.4 25.8 1.0
C2A B:HEC401 4.4 19.6 1.0
C3A B:HEC401 4.4 20.6 1.0
C2B B:HEC401 4.5 23.6 1.0
CG B:PRO112 4.8 26.3 1.0
CB B:PRO112 4.9 25.6 1.0
CD B:GLN108 5.0 22.4 1.0

Iron binding site 4 out of 4 in 6qkn

Go back to Iron Binding Sites List in 6qkn
Iron binding site 4 out of 4 in the Structure of the Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae


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 Azide-Inhibited Form of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:24.3
occ:1.00
FE B:HEC402 0.0 24.3 1.0
NB B:HEC402 2.0 20.6 1.0
ND B:HEC402 2.0 19.8 1.0
NC B:HEC402 2.1 20.2 1.0
NA B:HEC402 2.2 20.9 1.0
NE2 B:HIS204 2.2 28.1 1.0
SD B:MET280 2.3 40.4 1.0
C1B B:HEC402 3.0 20.9 1.0
C4D B:HEC402 3.0 21.1 1.0
C4B B:HEC402 3.0 21.7 1.0
C1D B:HEC402 3.0 19.0 1.0
C1C B:HEC402 3.1 20.3 1.0
C4C B:HEC402 3.1 19.2 1.0
CD2 B:HIS204 3.1 24.8 1.0
C1A B:HEC402 3.2 21.6 1.0
C4A B:HEC402 3.2 20.1 1.0
CE1 B:HIS204 3.2 29.7 1.0
CHB B:HEC402 3.4 20.9 1.0
CHD B:HEC402 3.4 19.8 1.0
CHA B:HEC402 3.4 22.4 1.0
CHC B:HEC402 3.4 19.5 1.0
CG B:MET280 3.5 29.3 1.0
CE B:MET280 3.6 30.4 1.0
C3B B:HEC402 4.3 21.8 1.0
CG B:HIS204 4.3 27.4 1.0
ND1 B:HIS204 4.3 29.6 1.0
C2B B:HEC402 4.3 20.9 1.0
C2D B:HEC402 4.3 19.3 1.0
C3D B:HEC402 4.3 19.7 1.0
C3C B:HEC402 4.4 20.5 1.0
C2C B:HEC402 4.4 21.3 1.0
CB B:MET280 4.4 25.9 1.0
C2A B:HEC402 4.5 21.4 1.0
C3A B:HEC402 4.5 20.9 1.0
CG B:GLN284 5.0 26.5 1.0

Reference:

A.L.Carvalho, M.J.Romao, S.Pauleta, C.Nobrega. Structure of the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae To Be Published.
Page generated: Wed Aug 7 08:00:22 2024

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