Iron in PDB 4b40: Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum
Enzymatic activity of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum
All present enzymatic activity of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum:
1.11.1.6;
Protein crystallography data
The structure of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum, PDB code: 4b40
was solved by
Y.Yuzugullu,
C.H.Trinh,
A.R.Pearson,
Z.B.Ogel,
M.J.Mcpherson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.41 /
1.93
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
201.726,
121.814,
125.435,
90.00,
115.10,
90.00
|
R / Rfree (%)
|
16.576 /
19.929
|
Other elements in 4b40:
The structure of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum
(pdb code 4b40). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum, PDB code: 4b40:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4b40
Go back to
Iron Binding Sites List in 4b40
Iron binding site 1 out
of 4 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe900
b:17.3
occ:1.00
|
FE
|
A:HDD900
|
0.0
|
17.3
|
1.0
|
OH
|
A:TYR369
|
1.9
|
15.3
|
1.0
|
ND
|
A:HDD900
|
1.9
|
16.8
|
1.0
|
NA
|
A:HDD900
|
2.1
|
16.1
|
1.0
|
NC
|
A:HDD900
|
2.1
|
17.2
|
1.0
|
NB
|
A:HDD900
|
2.1
|
16.7
|
1.0
|
O
|
A:HOH2095
|
2.6
|
11.9
|
0.3
|
C1D
|
A:HDD900
|
3.0
|
18.2
|
1.0
|
C4D
|
A:HDD900
|
3.0
|
16.9
|
1.0
|
CZ
|
A:TYR369
|
3.0
|
15.7
|
1.0
|
C4C
|
A:HDD900
|
3.0
|
17.4
|
1.0
|
C4A
|
A:HDD900
|
3.1
|
16.2
|
1.0
|
C1A
|
A:HDD900
|
3.1
|
16.2
|
1.0
|
C1B
|
A:HDD900
|
3.1
|
17.2
|
1.0
|
C4B
|
A:HDD900
|
3.1
|
17.0
|
1.0
|
C1C
|
A:HDD900
|
3.1
|
16.7
|
1.0
|
CHD
|
A:HDD900
|
3.4
|
16.9
|
1.0
|
CHA
|
A:HDD900
|
3.4
|
15.9
|
1.0
|
CHB
|
A:HDD900
|
3.4
|
16.0
|
1.0
|
CHC
|
A:HDD900
|
3.5
|
16.2
|
1.0
|
CE2
|
A:TYR369
|
3.8
|
16.1
|
1.0
|
CE1
|
A:TYR369
|
3.8
|
15.5
|
1.0
|
NE
|
A:ARG365
|
4.1
|
14.8
|
1.0
|
NH2
|
A:ARG365
|
4.2
|
15.4
|
1.0
|
C3D
|
A:HDD900
|
4.3
|
17.7
|
1.0
|
C2D
|
A:HDD900
|
4.3
|
18.5
|
1.0
|
C3C
|
A:HDD900
|
4.4
|
16.7
|
1.0
|
CG2
|
A:VAL81
|
4.4
|
14.7
|
1.0
|
C3A
|
A:HDD900
|
4.4
|
15.3
|
1.0
|
C2A
|
A:HDD900
|
4.4
|
15.1
|
1.0
|
C3B
|
A:HDD900
|
4.4
|
17.4
|
1.0
|
C2C
|
A:HDD900
|
4.4
|
16.7
|
1.0
|
O
|
A:HOH2094
|
4.5
|
22.1
|
1.0
|
C2B
|
A:HDD900
|
4.5
|
16.5
|
1.0
|
CZ
|
A:ARG365
|
4.6
|
14.7
|
1.0
|
CZ
|
A:PHE168
|
4.6
|
14.7
|
1.0
|
CD2
|
A:HIS82
|
4.8
|
14.1
|
1.0
|
O1D
|
A:HDD900
|
4.9
|
19.1
|
1.0
|
NE2
|
A:HIS82
|
5.0
|
15.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 4b40
Go back to
Iron Binding Sites List in 4b40
Iron binding site 2 out
of 4 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe900
b:16.3
occ:1.00
|
FE
|
B:HDD900
|
0.0
|
16.3
|
1.0
|
OH
|
B:TYR369
|
1.9
|
13.7
|
1.0
|
ND
|
B:HDD900
|
2.0
|
17.1
|
1.0
|
NC
|
B:HDD900
|
2.1
|
16.5
|
1.0
|
NA
|
B:HDD900
|
2.1
|
15.8
|
1.0
|
NB
|
B:HDD900
|
2.1
|
16.7
|
1.0
|
O
|
B:HOH2092
|
2.7
|
16.6
|
0.3
|
CZ
|
B:TYR369
|
3.0
|
13.8
|
1.0
|
C1D
|
B:HDD900
|
3.0
|
17.9
|
1.0
|
C4D
|
B:HDD900
|
3.0
|
17.2
|
1.0
|
C4C
|
B:HDD900
|
3.0
|
16.6
|
1.0
|
C4A
|
B:HDD900
|
3.1
|
15.6
|
1.0
|
C1A
|
B:HDD900
|
3.1
|
15.7
|
1.0
|
C4B
|
B:HDD900
|
3.1
|
15.7
|
1.0
|
C1C
|
B:HDD900
|
3.1
|
15.8
|
1.0
|
C1B
|
B:HDD900
|
3.1
|
16.4
|
1.0
|
CHD
|
B:HDD900
|
3.4
|
16.8
|
1.0
|
CHA
|
B:HDD900
|
3.4
|
16.2
|
1.0
|
CHB
|
B:HDD900
|
3.4
|
15.7
|
1.0
|
CHC
|
B:HDD900
|
3.5
|
15.7
|
1.0
|
CE2
|
B:TYR369
|
3.8
|
13.8
|
1.0
|
CE1
|
B:TYR369
|
3.8
|
14.6
|
1.0
|
NH2
|
B:ARG365
|
4.1
|
16.1
|
1.0
|
NE
|
B:ARG365
|
4.2
|
16.6
|
1.0
|
C3D
|
B:HDD900
|
4.3
|
18.3
|
1.0
|
C2D
|
B:HDD900
|
4.3
|
18.5
|
1.0
|
C3C
|
B:HDD900
|
4.3
|
16.2
|
1.0
|
C2A
|
B:HDD900
|
4.4
|
14.7
|
1.0
|
CG2
|
B:VAL81
|
4.4
|
14.9
|
1.0
|
O
|
B:HOH2091
|
4.4
|
22.0
|
1.0
|
C3A
|
B:HDD900
|
4.4
|
14.9
|
1.0
|
C3B
|
B:HDD900
|
4.4
|
15.8
|
1.0
|
C2C
|
B:HDD900
|
4.4
|
15.7
|
1.0
|
C2B
|
B:HDD900
|
4.5
|
15.5
|
1.0
|
CZ
|
B:PHE168
|
4.5
|
14.6
|
1.0
|
CZ
|
B:ARG365
|
4.6
|
16.6
|
1.0
|
CD2
|
B:HIS82
|
4.9
|
14.3
|
1.0
|
NE2
|
B:HIS82
|
5.0
|
15.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 4b40
Go back to
Iron Binding Sites List in 4b40
Iron binding site 3 out
of 4 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe900
b:15.6
occ:1.00
|
FE
|
C:HDD900
|
0.0
|
15.6
|
1.0
|
OH
|
C:TYR369
|
1.9
|
14.7
|
1.0
|
ND
|
C:HDD900
|
2.0
|
15.6
|
1.0
|
NC
|
C:HDD900
|
2.1
|
15.2
|
1.0
|
NA
|
C:HDD900
|
2.1
|
14.8
|
1.0
|
NB
|
C:HDD900
|
2.1
|
15.1
|
1.0
|
O
|
C:HOH2035
|
2.6
|
14.9
|
0.3
|
CZ
|
C:TYR369
|
3.0
|
14.3
|
1.0
|
C1D
|
C:HDD900
|
3.0
|
15.5
|
1.0
|
C4D
|
C:HDD900
|
3.0
|
15.5
|
1.0
|
C4C
|
C:HDD900
|
3.0
|
15.6
|
1.0
|
C1A
|
C:HDD900
|
3.1
|
14.2
|
1.0
|
C4A
|
C:HDD900
|
3.1
|
13.9
|
1.0
|
C4B
|
C:HDD900
|
3.1
|
15.3
|
1.0
|
C1B
|
C:HDD900
|
3.1
|
15.1
|
1.0
|
C1C
|
C:HDD900
|
3.1
|
14.8
|
1.0
|
CHD
|
C:HDD900
|
3.4
|
15.2
|
1.0
|
CHA
|
C:HDD900
|
3.4
|
13.9
|
1.0
|
CHB
|
C:HDD900
|
3.4
|
14.3
|
1.0
|
CHC
|
C:HDD900
|
3.5
|
15.3
|
1.0
|
CE1
|
C:TYR369
|
3.7
|
14.0
|
1.0
|
CE2
|
C:TYR369
|
3.8
|
14.3
|
1.0
|
NE
|
C:ARG365
|
4.1
|
14.6
|
1.0
|
NH2
|
C:ARG365
|
4.2
|
15.1
|
1.0
|
C3D
|
C:HDD900
|
4.3
|
16.5
|
1.0
|
C2D
|
C:HDD900
|
4.3
|
16.2
|
1.0
|
C3C
|
C:HDD900
|
4.4
|
16.0
|
1.0
|
C2A
|
C:HDD900
|
4.4
|
13.8
|
1.0
|
C3A
|
C:HDD900
|
4.4
|
13.9
|
1.0
|
CG2
|
C:VAL81
|
4.4
|
13.6
|
1.0
|
O
|
C:HOH2034
|
4.4
|
21.2
|
1.0
|
C3B
|
C:HDD900
|
4.4
|
15.6
|
1.0
|
C2C
|
C:HDD900
|
4.4
|
15.7
|
1.0
|
C2B
|
C:HDD900
|
4.5
|
15.2
|
1.0
|
CZ
|
C:ARG365
|
4.6
|
15.2
|
1.0
|
CZ
|
C:PHE168
|
4.6
|
15.8
|
1.0
|
CD2
|
C:HIS82
|
4.9
|
13.9
|
1.0
|
CD1
|
C:TYR369
|
5.0
|
13.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 4b40
Go back to
Iron Binding Sites List in 4b40
Iron binding site 4 out
of 4 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe900
b:15.9
occ:1.00
|
FE
|
D:HDD900
|
0.0
|
15.9
|
1.0
|
OH
|
D:TYR369
|
2.0
|
16.9
|
1.0
|
ND
|
D:HDD900
|
2.0
|
15.9
|
1.0
|
NC
|
D:HDD900
|
2.1
|
15.3
|
1.0
|
NA
|
D:HDD900
|
2.1
|
15.6
|
1.0
|
NB
|
D:HDD900
|
2.1
|
16.2
|
1.0
|
O
|
D:HOH2031
|
2.8
|
16.5
|
0.3
|
C1D
|
D:HDD900
|
3.0
|
16.0
|
1.0
|
CZ
|
D:TYR369
|
3.0
|
16.3
|
1.0
|
C4D
|
D:HDD900
|
3.0
|
15.8
|
1.0
|
C4C
|
D:HDD900
|
3.0
|
15.4
|
1.0
|
C4A
|
D:HDD900
|
3.1
|
14.8
|
1.0
|
C1A
|
D:HDD900
|
3.1
|
15.5
|
1.0
|
C1B
|
D:HDD900
|
3.1
|
16.1
|
1.0
|
C1C
|
D:HDD900
|
3.1
|
15.0
|
1.0
|
C4B
|
D:HDD900
|
3.1
|
15.8
|
1.0
|
CHD
|
D:HDD900
|
3.4
|
15.7
|
1.0
|
CHB
|
D:HDD900
|
3.4
|
15.2
|
1.0
|
CHA
|
D:HDD900
|
3.4
|
14.8
|
1.0
|
CHC
|
D:HDD900
|
3.5
|
14.5
|
1.0
|
CE2
|
D:TYR369
|
3.8
|
15.0
|
1.0
|
CE1
|
D:TYR369
|
3.8
|
16.3
|
1.0
|
NE
|
D:ARG365
|
4.2
|
13.4
|
1.0
|
NH2
|
D:ARG365
|
4.3
|
13.0
|
1.0
|
C2D
|
D:HDD900
|
4.3
|
16.9
|
1.0
|
C3D
|
D:HDD900
|
4.4
|
16.9
|
1.0
|
C3C
|
D:HDD900
|
4.4
|
15.4
|
1.0
|
C3A
|
D:HDD900
|
4.4
|
15.3
|
1.0
|
C2A
|
D:HDD900
|
4.4
|
14.7
|
1.0
|
CG2
|
D:VAL81
|
4.4
|
14.6
|
1.0
|
C3B
|
D:HDD900
|
4.4
|
16.1
|
1.0
|
C2C
|
D:HDD900
|
4.4
|
15.0
|
1.0
|
C2B
|
D:HDD900
|
4.4
|
16.0
|
1.0
|
O
|
D:HOH2032
|
4.5
|
22.6
|
1.0
|
CZ
|
D:PHE168
|
4.6
|
15.5
|
1.0
|
CZ
|
D:ARG365
|
4.6
|
13.7
|
1.0
|
CD2
|
D:HIS82
|
4.9
|
15.9
|
1.0
|
|
Reference:
Y.Yuzugullu,
C.H.Trinh,
L.Fairhurst,
Z.B.Ogel,
M.J.Mcpherson,
A.R.Pearson.
Investigating the Active Centre of the Scytalidium Thermophilum Catalase Acta Crystallogr.,Sect.F V. 69 369 2013.
ISSN: ISSN 1744-3091
PubMed: 23545640
DOI: 10.1107/S1744309113004211
Page generated: Sun Aug 4 23:56:42 2024
|