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:
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
|