Iron in PDB 7zs8: Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution
Enzymatic activity of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution
All present enzymatic activity of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution:
1.11.1.5;
Protein crystallography data
The structure of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution, PDB code: 7zs8
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)
|
39.95 /
1.40
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.842,
89.144,
89.731,
90,
90,
90
|
R / Rfree (%)
|
19.6 /
22.1
|
Other elements in 7zs8:
The structure of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution
(pdb code 7zs8). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution, PDB code: 7zs8:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7zs8
Go back to
Iron Binding Sites List in 7zs8
Iron binding site 1 out
of 4 in the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:11.5
occ:1.00
|
FE
|
A:HEC401
|
0.0
|
11.5
|
1.0
|
ND
|
A:HEC401
|
2.0
|
10.5
|
1.0
|
NA
|
A:HEC401
|
2.0
|
11.9
|
1.0
|
NE2
|
A:HIS59
|
2.0
|
10.3
|
1.0
|
NC
|
A:HEC401
|
2.0
|
12.5
|
1.0
|
NB
|
A:HEC401
|
2.0
|
10.1
|
1.0
|
O
|
A:HOH569
|
2.1
|
15.4
|
1.0
|
CE1
|
A:HIS59
|
3.0
|
11.4
|
1.0
|
C4D
|
A:HEC401
|
3.0
|
12.8
|
1.0
|
C1A
|
A:HEC401
|
3.0
|
11.4
|
1.0
|
C1C
|
A:HEC401
|
3.0
|
9.9
|
1.0
|
CD2
|
A:HIS59
|
3.0
|
11.5
|
1.0
|
C1D
|
A:HEC401
|
3.0
|
12.6
|
1.0
|
C4B
|
A:HEC401
|
3.0
|
10.0
|
1.0
|
C4C
|
A:HEC401
|
3.0
|
10.9
|
1.0
|
C4A
|
A:HEC401
|
3.1
|
11.1
|
1.0
|
C1B
|
A:HEC401
|
3.1
|
11.9
|
1.0
|
CHA
|
A:HEC401
|
3.3
|
11.1
|
1.0
|
CHD
|
A:HEC401
|
3.4
|
12.1
|
1.0
|
CHC
|
A:HEC401
|
3.4
|
10.8
|
1.0
|
CHB
|
A:HEC401
|
3.4
|
11.0
|
1.0
|
O
|
A:HOH578
|
4.0
|
21.2
|
1.0
|
NE2
|
A:GLN108
|
4.1
|
11.9
|
1.0
|
ND1
|
A:HIS59
|
4.1
|
10.8
|
1.0
|
CG
|
A:HIS59
|
4.1
|
11.2
|
1.0
|
C2C
|
A:HEC401
|
4.3
|
11.0
|
1.0
|
C2D
|
A:HEC401
|
4.3
|
13.4
|
1.0
|
C2A
|
A:HEC401
|
4.3
|
12.2
|
1.0
|
C3D
|
A:HEC401
|
4.3
|
13.1
|
1.0
|
C3C
|
A:HEC401
|
4.3
|
11.0
|
1.0
|
C3B
|
A:HEC401
|
4.3
|
11.2
|
1.0
|
C3A
|
A:HEC401
|
4.3
|
11.1
|
1.0
|
C2B
|
A:HEC401
|
4.4
|
10.4
|
1.0
|
CG
|
A:PRO112
|
4.6
|
12.6
|
1.0
|
CB
|
A:PRO112
|
4.8
|
12.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 7zs8
Go back to
Iron Binding Sites List in 7zs8
Iron binding site 2 out
of 4 in the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:14.8
occ:1.00
|
FE
|
A:HEC402
|
0.0
|
14.8
|
1.0
|
NE2
|
A:HIS204
|
2.0
|
13.2
|
1.0
|
ND
|
A:HEC402
|
2.0
|
13.3
|
1.0
|
NA
|
A:HEC402
|
2.0
|
14.8
|
1.0
|
NB
|
A:HEC402
|
2.1
|
15.9
|
1.0
|
NC
|
A:HEC402
|
2.1
|
14.9
|
1.0
|
SD
|
A:MET280
|
2.3
|
18.1
|
1.0
|
CE1
|
A:HIS204
|
3.0
|
13.5
|
1.0
|
CD2
|
A:HIS204
|
3.0
|
14.2
|
1.0
|
C1D
|
A:HEC402
|
3.0
|
14.1
|
1.0
|
C1B
|
A:HEC402
|
3.0
|
15.2
|
1.0
|
C1A
|
A:HEC402
|
3.0
|
13.5
|
1.0
|
C4D
|
A:HEC402
|
3.0
|
13.5
|
1.0
|
C4A
|
A:HEC402
|
3.0
|
15.3
|
1.0
|
C1C
|
A:HEC402
|
3.1
|
15.2
|
1.0
|
C4C
|
A:HEC402
|
3.1
|
16.0
|
1.0
|
C4B
|
A:HEC402
|
3.1
|
14.6
|
1.0
|
CHA
|
A:HEC402
|
3.4
|
15.3
|
1.0
|
CHB
|
A:HEC402
|
3.4
|
15.9
|
1.0
|
CHD
|
A:HEC402
|
3.4
|
15.3
|
1.0
|
CHC
|
A:HEC402
|
3.4
|
15.0
|
1.0
|
CG
|
A:MET280
|
3.4
|
19.8
|
1.0
|
CE
|
A:MET280
|
3.5
|
16.4
|
1.0
|
ND1
|
A:HIS204
|
4.1
|
13.6
|
1.0
|
CG
|
A:HIS204
|
4.2
|
13.1
|
1.0
|
C2D
|
A:HEC402
|
4.3
|
14.4
|
1.0
|
CB
|
A:MET280
|
4.3
|
17.3
|
1.0
|
C3D
|
A:HEC402
|
4.3
|
15.0
|
1.0
|
C2A
|
A:HEC402
|
4.3
|
13.1
|
1.0
|
C3B
|
A:HEC402
|
4.3
|
15.8
|
1.0
|
C3A
|
A:HEC402
|
4.3
|
14.8
|
1.0
|
C2B
|
A:HEC402
|
4.4
|
16.1
|
1.0
|
C3C
|
A:HEC402
|
4.4
|
16.0
|
1.0
|
C2C
|
A:HEC402
|
4.4
|
16.5
|
1.0
|
CG
|
A:GLN284
|
5.0
|
19.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 7zs8
Go back to
Iron Binding Sites List in 7zs8
Iron binding site 3 out
of 4 in the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:11.2
occ:1.00
|
FE
|
B:HEC401
|
0.0
|
11.2
|
1.0
|
NE2
|
B:HIS59
|
2.0
|
10.4
|
1.0
|
NA
|
B:HEC401
|
2.0
|
10.7
|
1.0
|
NC
|
B:HEC401
|
2.0
|
11.2
|
1.0
|
NB
|
B:HEC401
|
2.0
|
9.5
|
1.0
|
ND
|
B:HEC401
|
2.0
|
9.7
|
1.0
|
O
|
B:HOH571
|
2.1
|
13.8
|
1.0
|
CE1
|
B:HIS59
|
3.0
|
10.3
|
1.0
|
C1C
|
B:HEC401
|
3.0
|
9.2
|
1.0
|
C1A
|
B:HEC401
|
3.0
|
11.5
|
1.0
|
C4D
|
B:HEC401
|
3.0
|
10.2
|
1.0
|
C4C
|
B:HEC401
|
3.0
|
11.0
|
1.0
|
CD2
|
B:HIS59
|
3.0
|
11.5
|
1.0
|
C4A
|
B:HEC401
|
3.0
|
11.2
|
1.0
|
C1D
|
B:HEC401
|
3.0
|
10.4
|
1.0
|
C4B
|
B:HEC401
|
3.0
|
9.2
|
1.0
|
C1B
|
B:HEC401
|
3.0
|
10.6
|
1.0
|
CHB
|
B:HEC401
|
3.4
|
10.6
|
1.0
|
CHA
|
B:HEC401
|
3.4
|
11.4
|
1.0
|
CHC
|
B:HEC401
|
3.4
|
11.4
|
1.0
|
CHD
|
B:HEC401
|
3.4
|
11.8
|
1.0
|
OE1
|
B:GLN108
|
4.1
|
15.3
|
1.0
|
ND1
|
B:HIS59
|
4.1
|
9.1
|
1.0
|
CG
|
B:HIS59
|
4.1
|
9.5
|
1.0
|
C3C
|
B:HEC401
|
4.3
|
11.8
|
1.0
|
C2D
|
B:HEC401
|
4.3
|
11.5
|
1.0
|
C2C
|
B:HEC401
|
4.3
|
11.7
|
1.0
|
O
|
B:HOH540
|
4.3
|
25.6
|
1.0
|
C3A
|
B:HEC401
|
4.3
|
10.8
|
1.0
|
C3D
|
B:HEC401
|
4.3
|
11.1
|
1.0
|
C3B
|
B:HEC401
|
4.3
|
10.7
|
1.0
|
C2A
|
B:HEC401
|
4.3
|
11.1
|
1.0
|
C2B
|
B:HEC401
|
4.3
|
10.1
|
1.0
|
CG
|
B:PRO112
|
4.7
|
13.4
|
1.0
|
OE1
|
B:GLU118
|
4.8
|
26.6
|
1.0
|
CB
|
B:PRO112
|
4.9
|
13.4
|
1.0
|
CD
|
B:GLN108
|
5.0
|
13.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 7zs8
Go back to
Iron Binding Sites List in 7zs8
Iron binding site 4 out
of 4 in the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae at 1.4 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:12.4
occ:1.00
|
FE
|
B:HEC402
|
0.0
|
12.4
|
1.0
|
NA
|
B:HEC402
|
2.0
|
11.2
|
1.0
|
NB
|
B:HEC402
|
2.0
|
12.5
|
1.0
|
ND
|
B:HEC402
|
2.0
|
11.7
|
1.0
|
NC
|
B:HEC402
|
2.1
|
11.7
|
1.0
|
NE2
|
B:HIS204
|
2.1
|
12.7
|
1.0
|
SD
|
B:MET280
|
2.4
|
15.5
|
1.0
|
C1A
|
B:HEC402
|
3.0
|
11.1
|
1.0
|
C4D
|
B:HEC402
|
3.0
|
10.9
|
1.0
|
CD2
|
B:HIS204
|
3.0
|
11.6
|
1.0
|
C4A
|
B:HEC402
|
3.0
|
11.5
|
1.0
|
C1D
|
B:HEC402
|
3.0
|
12.9
|
1.0
|
C1B
|
B:HEC402
|
3.1
|
12.5
|
1.0
|
C4C
|
B:HEC402
|
3.1
|
13.0
|
1.0
|
C4B
|
B:HEC402
|
3.1
|
13.2
|
1.0
|
C1C
|
B:HEC402
|
3.1
|
14.1
|
1.0
|
CE1
|
B:HIS204
|
3.1
|
12.0
|
1.0
|
CHA
|
B:HEC402
|
3.4
|
12.7
|
1.0
|
CE
|
B:MET280
|
3.4
|
13.3
|
1.0
|
CHB
|
B:HEC402
|
3.4
|
12.4
|
1.0
|
CG
|
B:MET280
|
3.4
|
16.4
|
1.0
|
CHD
|
B:HEC402
|
3.4
|
12.9
|
1.0
|
CHC
|
B:HEC402
|
3.5
|
13.1
|
1.0
|
ND1
|
B:HIS204
|
4.2
|
12.6
|
1.0
|
CG
|
B:HIS204
|
4.2
|
12.5
|
1.0
|
CB
|
B:MET280
|
4.3
|
15.5
|
1.0
|
C2A
|
B:HEC402
|
4.3
|
12.2
|
1.0
|
C3A
|
B:HEC402
|
4.3
|
11.6
|
1.0
|
C2D
|
B:HEC402
|
4.3
|
12.9
|
1.0
|
C3D
|
B:HEC402
|
4.3
|
12.2
|
1.0
|
C3C
|
B:HEC402
|
4.3
|
13.6
|
1.0
|
C2C
|
B:HEC402
|
4.3
|
14.2
|
1.0
|
C2B
|
B:HEC402
|
4.3
|
13.1
|
1.0
|
C3B
|
B:HEC402
|
4.4
|
13.3
|
1.0
|
CG
|
B:GLN284
|
4.9
|
13.3
|
1.0
|
|
Reference:
C.S.Nobrega,
A.L.Carvalho,
M.J.Romao,
S.R.Pauleta.
Structural Characterization of Neisseria Gonorrhoeae Bacterial Peroxidase - Insights Into the Catalytic Cycle of Bacterial Peroxidases Int J Mol Sci 2023.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS24076246
Page generated: Fri Aug 9 15:20:08 2024
|