Iron in PDB 6fu3: Structure of the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae
Enzymatic activity of Structure of the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae
All present enzymatic activity of Structure of the Mixed-Valence, Active 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 Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae, PDB code: 6fu3
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)
|
64.26 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.942,
88.780,
93.122,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.7 /
25.5
|
Other elements in 6fu3:
The structure of Structure of the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of the Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae
(pdb code 6fu3). 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 Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae, PDB code: 6fu3:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6fu3
Go back to
Iron Binding Sites List in 6fu3
Iron binding site 1 out
of 4 in the Structure of the Mixed-Valence, Active 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 Mixed-Valence, Active 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:13.0
occ:1.00
|
FE
|
A:HEC402
|
0.0
|
13.0
|
1.0
|
NB
|
A:HEC402
|
2.0
|
12.1
|
1.0
|
NA
|
A:HEC402
|
2.0
|
11.2
|
1.0
|
NE2
|
A:HIS59
|
2.0
|
12.3
|
1.0
|
ND
|
A:HEC402
|
2.1
|
12.3
|
1.0
|
NC
|
A:HEC402
|
2.1
|
12.2
|
1.0
|
O
|
A:HOH633
|
2.2
|
11.6
|
1.0
|
C1B
|
A:HEC402
|
2.9
|
11.5
|
1.0
|
C4A
|
A:HEC402
|
2.9
|
10.5
|
1.0
|
C4B
|
A:HEC402
|
3.0
|
11.6
|
1.0
|
C1A
|
A:HEC402
|
3.0
|
10.4
|
1.0
|
C4D
|
A:HEC402
|
3.0
|
11.4
|
1.0
|
CE1
|
A:HIS59
|
3.0
|
11.9
|
1.0
|
CD2
|
A:HIS59
|
3.0
|
12.1
|
1.0
|
C1D
|
A:HEC402
|
3.1
|
12.8
|
1.0
|
C1C
|
A:HEC402
|
3.1
|
11.2
|
1.0
|
C4C
|
A:HEC402
|
3.1
|
10.9
|
1.0
|
CHB
|
A:HEC402
|
3.2
|
11.0
|
1.0
|
CHA
|
A:HEC402
|
3.3
|
10.9
|
1.0
|
CHC
|
A:HEC402
|
3.3
|
11.3
|
1.0
|
CHD
|
A:HEC402
|
3.4
|
12.7
|
1.0
|
O
|
A:HOH532
|
3.9
|
24.7
|
1.0
|
C2B
|
A:HEC402
|
4.0
|
11.1
|
1.0
|
C3A
|
A:HEC402
|
4.1
|
10.8
|
1.0
|
C3B
|
A:HEC402
|
4.1
|
11.3
|
1.0
|
NE2
|
A:GLN108
|
4.1
|
11.1
|
1.0
|
C2A
|
A:HEC402
|
4.1
|
10.9
|
1.0
|
ND1
|
A:HIS59
|
4.1
|
11.1
|
1.0
|
C3D
|
A:HEC402
|
4.1
|
12.7
|
1.0
|
C2D
|
A:HEC402
|
4.1
|
12.2
|
1.0
|
CG
|
A:HIS59
|
4.2
|
11.1
|
1.0
|
C2C
|
A:HEC402
|
4.2
|
11.1
|
1.0
|
C3C
|
A:HEC402
|
4.2
|
11.6
|
1.0
|
CG
|
A:PRO112
|
4.6
|
11.5
|
1.0
|
CB
|
A:PRO112
|
4.9
|
11.8
|
1.0
|
OE1
|
A:GLU118
|
4.9
|
28.8
|
1.0
|
CD
|
A:GLN108
|
5.0
|
11.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 6fu3
Go back to
Iron Binding Sites List in 6fu3
Iron binding site 2 out
of 4 in the Structure of the Mixed-Valence, Active 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 Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe403
b:16.5
occ:1.00
|
FE
|
A:HEC403
|
0.0
|
16.5
|
1.0
|
NC
|
A:HEC403
|
2.0
|
14.8
|
1.0
|
NB
|
A:HEC403
|
2.0
|
15.5
|
1.0
|
ND
|
A:HEC403
|
2.0
|
13.8
|
1.0
|
NE2
|
A:HIS204
|
2.1
|
14.8
|
1.0
|
NA
|
A:HEC403
|
2.1
|
12.6
|
1.0
|
SD
|
A:MET280
|
2.3
|
16.4
|
1.0
|
C1D
|
A:HEC403
|
3.0
|
14.0
|
1.0
|
C4C
|
A:HEC403
|
3.0
|
15.4
|
1.0
|
C1B
|
A:HEC403
|
3.0
|
14.4
|
1.0
|
CD2
|
A:HIS204
|
3.0
|
15.4
|
1.0
|
C1C
|
A:HEC403
|
3.0
|
14.8
|
1.0
|
C4B
|
A:HEC403
|
3.0
|
14.9
|
1.0
|
C4A
|
A:HEC403
|
3.0
|
13.5
|
1.0
|
C4D
|
A:HEC403
|
3.1
|
14.3
|
1.0
|
C1A
|
A:HEC403
|
3.1
|
12.6
|
1.0
|
CE1
|
A:HIS204
|
3.1
|
14.2
|
1.0
|
CHD
|
A:HEC403
|
3.3
|
14.5
|
1.0
|
CHB
|
A:HEC403
|
3.3
|
13.8
|
1.0
|
CHC
|
A:HEC403
|
3.3
|
14.1
|
1.0
|
CG
|
A:MET280
|
3.4
|
16.2
|
1.0
|
CHA
|
A:HEC403
|
3.4
|
12.4
|
1.0
|
CE
|
A:MET280
|
3.5
|
16.7
|
1.0
|
C2D
|
A:HEC403
|
4.1
|
14.4
|
1.0
|
C2B
|
A:HEC403
|
4.1
|
15.9
|
1.0
|
C3C
|
A:HEC403
|
4.1
|
15.1
|
1.0
|
C2C
|
A:HEC403
|
4.1
|
14.5
|
1.0
|
C3D
|
A:HEC403
|
4.1
|
14.5
|
1.0
|
C3B
|
A:HEC403
|
4.2
|
15.1
|
1.0
|
C3A
|
A:HEC403
|
4.2
|
13.5
|
1.0
|
CG
|
A:HIS204
|
4.2
|
14.8
|
1.0
|
C2A
|
A:HEC403
|
4.2
|
13.4
|
1.0
|
ND1
|
A:HIS204
|
4.2
|
14.1
|
1.0
|
CB
|
A:MET280
|
4.2
|
16.9
|
1.0
|
CG
|
A:GLN284
|
4.9
|
20.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 6fu3
Go back to
Iron Binding Sites List in 6fu3
Iron binding site 3 out
of 4 in the Structure of the Mixed-Valence, Active 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 Mixed-Valence, Active 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:13.9
occ:1.00
|
FE
|
B:HEC402
|
0.0
|
13.9
|
1.0
|
NE2
|
B:HIS59
|
1.9
|
11.5
|
1.0
|
NA
|
B:HEC402
|
2.0
|
13.5
|
1.0
|
ND
|
B:HEC402
|
2.0
|
13.8
|
1.0
|
NC
|
B:HEC402
|
2.1
|
14.0
|
1.0
|
NB
|
B:HEC402
|
2.1
|
12.9
|
1.0
|
O
|
B:HOH635
|
2.1
|
12.7
|
1.0
|
CE1
|
B:HIS59
|
2.9
|
12.0
|
1.0
|
C1D
|
B:HEC402
|
3.0
|
14.1
|
1.0
|
CD2
|
B:HIS59
|
3.0
|
11.7
|
1.0
|
C4D
|
B:HEC402
|
3.0
|
13.4
|
1.0
|
C4C
|
B:HEC402
|
3.0
|
13.3
|
1.0
|
C4A
|
B:HEC402
|
3.0
|
12.2
|
1.0
|
C1A
|
B:HEC402
|
3.0
|
12.6
|
1.0
|
C4B
|
B:HEC402
|
3.1
|
12.8
|
1.0
|
C1B
|
B:HEC402
|
3.1
|
13.7
|
1.0
|
C1C
|
B:HEC402
|
3.1
|
11.9
|
1.0
|
CHD
|
B:HEC402
|
3.3
|
13.6
|
1.0
|
CHB
|
B:HEC402
|
3.4
|
13.3
|
1.0
|
CHA
|
B:HEC402
|
3.4
|
12.0
|
1.0
|
CHC
|
B:HEC402
|
3.5
|
11.8
|
1.0
|
ND1
|
B:HIS59
|
4.0
|
11.4
|
1.0
|
CG
|
B:HIS59
|
4.1
|
11.7
|
1.0
|
NE2
|
B:GLN108
|
4.1
|
14.8
|
1.0
|
C2D
|
B:HEC402
|
4.3
|
13.4
|
1.0
|
C3B
|
B:HEC402
|
4.3
|
13.0
|
1.0
|
C3D
|
B:HEC402
|
4.3
|
13.3
|
1.0
|
C3C
|
B:HEC402
|
4.3
|
12.6
|
1.0
|
C2A
|
B:HEC402
|
4.3
|
11.5
|
1.0
|
C3A
|
B:HEC402
|
4.4
|
12.0
|
1.0
|
C2B
|
B:HEC402
|
4.4
|
12.2
|
1.0
|
O
|
B:HOH591
|
4.4
|
22.9
|
1.0
|
C2C
|
B:HEC402
|
4.4
|
11.9
|
1.0
|
OE1
|
B:GLU118
|
4.6
|
21.1
|
1.0
|
CG
|
B:PRO112
|
4.7
|
13.4
|
1.0
|
CB
|
B:PRO112
|
4.9
|
14.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 6fu3
Go back to
Iron Binding Sites List in 6fu3
Iron binding site 4 out
of 4 in the Structure of the Mixed-Valence, Active 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 Mixed-Valence, Active Form, of Cytochrome C Peroxidase From Obligate Human Pathogenic Bacterium Neisseria Gonorrhoeae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe403
b:15.1
occ:1.00
|
FE
|
B:HEC403
|
0.0
|
15.1
|
1.0
|
ND
|
B:HEC403
|
2.0
|
12.3
|
1.0
|
NB
|
B:HEC403
|
2.0
|
14.0
|
1.0
|
NA
|
B:HEC403
|
2.1
|
12.8
|
1.0
|
NC
|
B:HEC403
|
2.1
|
15.2
|
1.0
|
NE2
|
B:HIS204
|
2.1
|
15.4
|
1.0
|
SD
|
B:MET280
|
2.3
|
14.1
|
1.0
|
C4D
|
B:HEC403
|
3.0
|
12.4
|
1.0
|
C4B
|
B:HEC403
|
3.0
|
14.1
|
1.0
|
CD2
|
B:HIS204
|
3.0
|
15.3
|
1.0
|
C4A
|
B:HEC403
|
3.1
|
12.2
|
1.0
|
C1D
|
B:HEC403
|
3.1
|
13.6
|
1.0
|
C1A
|
B:HEC403
|
3.1
|
11.5
|
1.0
|
C1C
|
B:HEC403
|
3.1
|
13.5
|
1.0
|
C4C
|
B:HEC403
|
3.1
|
13.6
|
1.0
|
C1B
|
B:HEC403
|
3.1
|
14.9
|
1.0
|
CE1
|
B:HIS204
|
3.2
|
14.1
|
1.0
|
CHA
|
B:HEC403
|
3.3
|
10.5
|
1.0
|
CG
|
B:MET280
|
3.4
|
13.6
|
1.0
|
CHB
|
B:HEC403
|
3.4
|
12.7
|
1.0
|
CHC
|
B:HEC403
|
3.4
|
13.2
|
1.0
|
CE
|
B:MET280
|
3.4
|
13.7
|
1.0
|
CHD
|
B:HEC403
|
3.5
|
12.5
|
1.0
|
CG
|
B:HIS204
|
4.2
|
14.8
|
1.0
|
ND1
|
B:HIS204
|
4.3
|
14.2
|
1.0
|
C3D
|
B:HEC403
|
4.3
|
12.3
|
1.0
|
CB
|
B:MET280
|
4.3
|
14.3
|
1.0
|
C3B
|
B:HEC403
|
4.3
|
13.6
|
1.0
|
C2D
|
B:HEC403
|
4.3
|
12.3
|
1.0
|
C3C
|
B:HEC403
|
4.4
|
14.7
|
1.0
|
C3A
|
B:HEC403
|
4.4
|
11.6
|
1.0
|
C2A
|
B:HEC403
|
4.4
|
12.0
|
1.0
|
C2C
|
B:HEC403
|
4.4
|
13.9
|
1.0
|
C2B
|
B:HEC403
|
4.4
|
13.3
|
1.0
|
CG
|
B:GLN284
|
4.9
|
15.7
|
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: Tue Aug 6 18:39:48 2024
|