Iron in PDB 8pwy: Dye-Decolourising Peroxidase Dtpb (112 Kgy)
Protein crystallography data
The structure of Dye-Decolourising Peroxidase Dtpb (112 Kgy), PDB code: 8pwy
was solved by
M.Lucic,
J.A.R.Worrall,
M.A.Hough,
R.L.Owen,
R.W.Strange,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
40.07 /
1.80
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.771,
121.825,
199.518,
90,
90,
90
|
|
R / Rfree (%)
|
19.8 /
22.3
|
Other elements in 8pwy:
The structure of Dye-Decolourising Peroxidase Dtpb (112 Kgy) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Dye-Decolourising Peroxidase Dtpb (112 Kgy)
(pdb code 8pwy). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Dye-Decolourising Peroxidase Dtpb (112 Kgy), PDB code: 8pwy:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8pwy
Go back to
Iron Binding Sites List in 8pwy
Iron binding site 1 out
of 6 in the Dye-Decolourising Peroxidase Dtpb (112 Kgy)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Dye-Decolourising Peroxidase Dtpb (112 Kgy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:20.0
occ:1.00
|
FE
|
A:HEM402
|
0.0
|
20.0
|
1.0
|
|
O
|
A:O401
|
1.9
|
18.4
|
0.8
|
|
ND
|
A:HEM402
|
2.0
|
19.8
|
1.0
|
|
NA
|
A:HEM402
|
2.0
|
23.6
|
1.0
|
|
NC
|
A:HEM402
|
2.1
|
20.2
|
1.0
|
|
NE2
|
A:HIS225
|
2.1
|
17.5
|
1.0
|
|
NB
|
A:HEM402
|
2.1
|
27.4
|
1.0
|
|
C4D
|
A:HEM402
|
3.0
|
22.3
|
1.0
|
|
C1D
|
A:HEM402
|
3.0
|
21.4
|
1.0
|
|
C1A
|
A:HEM402
|
3.0
|
24.0
|
1.0
|
|
C4C
|
A:HEM402
|
3.0
|
21.1
|
1.0
|
|
C4A
|
A:HEM402
|
3.1
|
20.9
|
1.0
|
|
C1B
|
A:HEM402
|
3.1
|
26.0
|
1.0
|
|
CE1
|
A:HIS225
|
3.1
|
19.4
|
1.0
|
|
C4B
|
A:HEM402
|
3.1
|
24.3
|
1.0
|
|
CD2
|
A:HIS225
|
3.1
|
20.2
|
1.0
|
|
C1C
|
A:HEM402
|
3.1
|
22.0
|
1.0
|
|
CHD
|
A:HEM402
|
3.4
|
20.9
|
1.0
|
|
CHA
|
A:HEM402
|
3.4
|
21.6
|
1.0
|
|
CHB
|
A:HEM402
|
3.4
|
22.5
|
1.0
|
|
CHC
|
A:HEM402
|
3.5
|
20.2
|
1.0
|
|
NH1
|
A:ARG243
|
3.9
|
24.1
|
1.0
|
|
ND1
|
A:HIS225
|
4.2
|
18.3
|
1.0
|
|
C3A
|
A:HEM402
|
4.2
|
24.4
|
1.0
|
|
C2A
|
A:HEM402
|
4.2
|
24.0
|
1.0
|
|
CG
|
A:HIS225
|
4.2
|
20.2
|
1.0
|
|
C2D
|
A:HEM402
|
4.3
|
22.1
|
1.0
|
|
C3D
|
A:HEM402
|
4.3
|
22.8
|
1.0
|
|
C2B
|
A:HEM402
|
4.3
|
26.7
|
1.0
|
|
C3C
|
A:HEM402
|
4.3
|
20.7
|
1.0
|
|
C3B
|
A:HEM402
|
4.3
|
27.0
|
1.0
|
|
C2C
|
A:HEM402
|
4.3
|
22.8
|
1.0
|
|
CD
|
A:ARG243
|
4.4
|
22.1
|
1.0
|
|
ND2
|
A:ASN245
|
4.5
|
27.1
|
1.0
|
|
CZ
|
A:ARG243
|
4.7
|
27.0
|
1.0
|
|
NE
|
A:ARG243
|
4.8
|
24.9
|
1.0
|
|
Iron binding site 2 out
of 6 in 8pwy
Go back to
Iron Binding Sites List in 8pwy
Iron binding site 2 out
of 6 in the Dye-Decolourising Peroxidase Dtpb (112 Kgy)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Dye-Decolourising Peroxidase Dtpb (112 Kgy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:20.0
occ:1.00
|
FE
|
B:HEM402
|
0.0
|
20.0
|
1.0
|
|
O
|
B:O401
|
1.8
|
19.9
|
0.6
|
|
ND
|
B:HEM402
|
1.9
|
20.6
|
1.0
|
|
NA
|
B:HEM402
|
1.9
|
16.4
|
1.0
|
|
NC
|
B:HEM402
|
2.0
|
18.3
|
1.0
|
|
NB
|
B:HEM402
|
2.1
|
20.7
|
1.0
|
|
NE2
|
B:HIS225
|
2.1
|
19.6
|
1.0
|
|
C1D
|
B:HEM402
|
2.9
|
18.9
|
1.0
|
|
C4C
|
B:HEM402
|
2.9
|
18.1
|
1.0
|
|
C1A
|
B:HEM402
|
3.0
|
18.9
|
1.0
|
|
C4A
|
B:HEM402
|
3.0
|
18.4
|
1.0
|
|
C4D
|
B:HEM402
|
3.0
|
19.3
|
1.0
|
|
C1B
|
B:HEM402
|
3.0
|
20.1
|
1.0
|
|
CE1
|
B:HIS225
|
3.1
|
21.2
|
1.0
|
|
C1C
|
B:HEM402
|
3.1
|
20.4
|
1.0
|
|
C4B
|
B:HEM402
|
3.1
|
21.9
|
1.0
|
|
CD2
|
B:HIS225
|
3.1
|
19.5
|
1.0
|
|
CHD
|
B:HEM402
|
3.3
|
19.9
|
1.0
|
|
CHB
|
B:HEM402
|
3.4
|
18.7
|
1.0
|
|
CHA
|
B:HEM402
|
3.4
|
19.6
|
1.0
|
|
CHC
|
B:HEM402
|
3.5
|
21.5
|
1.0
|
|
NH1
|
B:ARG243
|
4.1
|
23.7
|
1.0
|
|
C3A
|
B:HEM402
|
4.2
|
17.5
|
1.0
|
|
C2A
|
B:HEM402
|
4.2
|
18.1
|
1.0
|
|
C3D
|
B:HEM402
|
4.2
|
19.4
|
1.0
|
|
ND1
|
B:HIS225
|
4.2
|
20.0
|
1.0
|
|
C3C
|
B:HEM402
|
4.2
|
18.8
|
1.0
|
|
C2D
|
B:HEM402
|
4.2
|
19.4
|
1.0
|
|
C2C
|
B:HEM402
|
4.2
|
18.3
|
1.0
|
|
CG
|
B:HIS225
|
4.3
|
19.9
|
1.0
|
|
C2B
|
B:HEM402
|
4.3
|
20.3
|
1.0
|
|
C3B
|
B:HEM402
|
4.3
|
21.5
|
1.0
|
|
CD
|
B:ARG243
|
4.4
|
23.3
|
1.0
|
|
ND2
|
B:ASN245
|
4.4
|
27.1
|
1.0
|
|
CZ
|
B:ARG243
|
4.8
|
25.3
|
1.0
|
|
NE
|
B:ARG243
|
4.8
|
22.7
|
1.0
|
|
Iron binding site 3 out
of 6 in 8pwy
Go back to
Iron Binding Sites List in 8pwy
Iron binding site 3 out
of 6 in the Dye-Decolourising Peroxidase Dtpb (112 Kgy)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Dye-Decolourising Peroxidase Dtpb (112 Kgy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:24.0
occ:1.00
|
FE
|
C:HEM402
|
0.0
|
24.0
|
1.0
|
|
ND
|
C:HEM402
|
2.0
|
23.0
|
1.0
|
|
NA
|
C:HEM402
|
2.0
|
24.1
|
1.0
|
|
O
|
C:O401
|
2.0
|
25.0
|
0.8
|
|
NC
|
C:HEM402
|
2.0
|
20.5
|
1.0
|
|
NB
|
C:HEM402
|
2.1
|
25.8
|
1.0
|
|
NE2
|
C:HIS225
|
2.1
|
23.3
|
1.0
|
|
C4D
|
C:HEM402
|
3.0
|
22.6
|
1.0
|
|
C4C
|
C:HEM402
|
3.0
|
23.8
|
1.0
|
|
C1B
|
C:HEM402
|
3.0
|
27.8
|
1.0
|
|
C4A
|
C:HEM402
|
3.0
|
26.8
|
1.0
|
|
C1D
|
C:HEM402
|
3.1
|
22.5
|
1.0
|
|
C1A
|
C:HEM402
|
3.1
|
23.8
|
1.0
|
|
C4B
|
C:HEM402
|
3.1
|
23.9
|
1.0
|
|
CE1
|
C:HIS225
|
3.1
|
27.4
|
1.0
|
|
C1C
|
C:HEM402
|
3.1
|
23.5
|
1.0
|
|
CD2
|
C:HIS225
|
3.2
|
24.6
|
1.0
|
|
CHB
|
C:HEM402
|
3.4
|
24.8
|
1.0
|
|
CHD
|
C:HEM402
|
3.4
|
22.3
|
1.0
|
|
CHA
|
C:HEM402
|
3.5
|
21.7
|
1.0
|
|
CHC
|
C:HEM402
|
3.5
|
21.0
|
1.0
|
|
NH1
|
C:ARG243
|
4.0
|
23.3
|
1.0
|
|
C3A
|
C:HEM402
|
4.2
|
26.8
|
1.0
|
|
ND1
|
C:HIS225
|
4.2
|
24.6
|
1.0
|
|
C2A
|
C:HEM402
|
4.2
|
26.3
|
1.0
|
|
C3D
|
C:HEM402
|
4.2
|
23.4
|
1.0
|
|
C3C
|
C:HEM402
|
4.3
|
23.4
|
1.0
|
|
C2D
|
C:HEM402
|
4.3
|
23.1
|
1.0
|
|
CG
|
C:HIS225
|
4.3
|
24.0
|
1.0
|
|
C3B
|
C:HEM402
|
4.3
|
24.1
|
1.0
|
|
C2B
|
C:HEM402
|
4.3
|
27.9
|
1.0
|
|
C2C
|
C:HEM402
|
4.3
|
22.2
|
1.0
|
|
CD
|
C:ARG243
|
4.4
|
23.6
|
1.0
|
|
ND2
|
C:ASN245
|
4.5
|
32.8
|
1.0
|
|
CZ
|
C:ARG243
|
4.7
|
27.9
|
1.0
|
|
NE
|
C:ARG243
|
4.9
|
25.6
|
1.0
|
|
Iron binding site 4 out
of 6 in 8pwy
Go back to
Iron Binding Sites List in 8pwy
Iron binding site 4 out
of 6 in the Dye-Decolourising Peroxidase Dtpb (112 Kgy)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Dye-Decolourising Peroxidase Dtpb (112 Kgy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe402
b:17.8
occ:1.00
|
FE
|
D:HEM402
|
0.0
|
17.8
|
1.0
|
|
ND
|
D:HEM402
|
1.9
|
17.7
|
1.0
|
|
O
|
D:O401
|
1.9
|
16.8
|
0.7
|
|
NA
|
D:HEM402
|
2.0
|
18.7
|
1.0
|
|
NB
|
D:HEM402
|
2.0
|
19.6
|
1.0
|
|
NC
|
D:HEM402
|
2.0
|
17.2
|
1.0
|
|
NE2
|
D:HIS225
|
2.1
|
19.0
|
1.0
|
|
C1D
|
D:HEM402
|
2.9
|
16.9
|
1.0
|
|
C4D
|
D:HEM402
|
3.0
|
15.8
|
1.0
|
|
C4B
|
D:HEM402
|
3.0
|
20.3
|
1.0
|
|
C4C
|
D:HEM402
|
3.0
|
16.8
|
1.0
|
|
C1A
|
D:HEM402
|
3.0
|
18.1
|
1.0
|
|
C1C
|
D:HEM402
|
3.0
|
18.7
|
1.0
|
|
C4A
|
D:HEM402
|
3.0
|
17.0
|
1.0
|
|
C1B
|
D:HEM402
|
3.1
|
20.5
|
1.0
|
|
CE1
|
D:HIS225
|
3.1
|
17.8
|
1.0
|
|
CD2
|
D:HIS225
|
3.2
|
20.5
|
1.0
|
|
CHD
|
D:HEM402
|
3.3
|
15.9
|
1.0
|
|
CHC
|
D:HEM402
|
3.4
|
17.9
|
1.0
|
|
CHA
|
D:HEM402
|
3.4
|
16.1
|
1.0
|
|
CHB
|
D:HEM402
|
3.4
|
18.5
|
1.0
|
|
NH1
|
D:ARG243
|
4.0
|
19.2
|
1.0
|
|
C3C
|
D:HEM402
|
4.2
|
16.6
|
1.0
|
|
C2C
|
D:HEM402
|
4.2
|
17.1
|
1.0
|
|
C3D
|
D:HEM402
|
4.2
|
17.4
|
1.0
|
|
C2D
|
D:HEM402
|
4.2
|
17.7
|
1.0
|
|
ND1
|
D:HIS225
|
4.2
|
16.7
|
1.0
|
|
C3A
|
D:HEM402
|
4.3
|
17.5
|
1.0
|
|
C2A
|
D:HEM402
|
4.3
|
18.2
|
1.0
|
|
CG
|
D:HIS225
|
4.3
|
17.8
|
1.0
|
|
C3B
|
D:HEM402
|
4.3
|
21.6
|
1.0
|
|
C2B
|
D:HEM402
|
4.3
|
21.1
|
1.0
|
|
CD
|
D:ARG243
|
4.4
|
22.8
|
1.0
|
|
ND2
|
D:ASN245
|
4.4
|
25.1
|
1.0
|
|
CZ
|
D:ARG243
|
4.7
|
20.9
|
1.0
|
|
NE
|
D:ARG243
|
4.8
|
23.6
|
1.0
|
|
Iron binding site 5 out
of 6 in 8pwy
Go back to
Iron Binding Sites List in 8pwy
Iron binding site 5 out
of 6 in the Dye-Decolourising Peroxidase Dtpb (112 Kgy)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Dye-Decolourising Peroxidase Dtpb (112 Kgy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe402
b:22.4
occ:1.00
|
FE
|
E:HEM402
|
0.0
|
22.4
|
1.0
|
|
ND
|
E:HEM402
|
1.9
|
22.1
|
1.0
|
|
O
|
E:O401
|
2.0
|
24.0
|
0.7
|
|
NA
|
E:HEM402
|
2.0
|
21.5
|
1.0
|
|
NB
|
E:HEM402
|
2.1
|
23.8
|
1.0
|
|
NC
|
E:HEM402
|
2.1
|
22.6
|
1.0
|
|
NE2
|
E:HIS225
|
2.1
|
23.5
|
1.0
|
|
C4D
|
E:HEM402
|
2.9
|
22.2
|
1.0
|
|
C1D
|
E:HEM402
|
2.9
|
21.2
|
1.0
|
|
C1A
|
E:HEM402
|
3.0
|
20.1
|
1.0
|
|
C4A
|
E:HEM402
|
3.0
|
22.0
|
1.0
|
|
C4B
|
E:HEM402
|
3.0
|
26.2
|
1.0
|
|
CE1
|
E:HIS225
|
3.0
|
27.0
|
1.0
|
|
C4C
|
E:HEM402
|
3.0
|
20.7
|
1.0
|
|
C1B
|
E:HEM402
|
3.1
|
22.7
|
1.0
|
|
C1C
|
E:HEM402
|
3.1
|
21.7
|
1.0
|
|
CD2
|
E:HIS225
|
3.1
|
23.7
|
1.0
|
|
CHA
|
E:HEM402
|
3.3
|
21.9
|
1.0
|
|
CHD
|
E:HEM402
|
3.4
|
21.4
|
1.0
|
|
CHC
|
E:HEM402
|
3.4
|
23.5
|
1.0
|
|
CHB
|
E:HEM402
|
3.4
|
23.4
|
1.0
|
|
NH1
|
E:ARG243
|
4.0
|
23.9
|
1.0
|
|
C2D
|
E:HEM402
|
4.2
|
21.4
|
1.0
|
|
C3D
|
E:HEM402
|
4.2
|
20.8
|
1.0
|
|
ND1
|
E:HIS225
|
4.2
|
25.8
|
1.0
|
|
C3A
|
E:HEM402
|
4.2
|
21.2
|
1.0
|
|
C2A
|
E:HEM402
|
4.2
|
19.8
|
1.0
|
|
CG
|
E:HIS225
|
4.2
|
26.6
|
1.0
|
|
C2C
|
E:HEM402
|
4.3
|
20.2
|
1.0
|
|
C2B
|
E:HEM402
|
4.3
|
21.0
|
1.0
|
|
C3C
|
E:HEM402
|
4.3
|
23.4
|
1.0
|
|
C3B
|
E:HEM402
|
4.3
|
24.3
|
1.0
|
|
ND2
|
E:ASN245
|
4.3
|
28.3
|
1.0
|
|
CD
|
E:ARG243
|
4.4
|
25.0
|
1.0
|
|
CZ
|
E:ARG243
|
4.7
|
25.4
|
1.0
|
|
NE
|
E:ARG243
|
4.8
|
24.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 8pwy
Go back to
Iron Binding Sites List in 8pwy
Iron binding site 6 out
of 6 in the Dye-Decolourising Peroxidase Dtpb (112 Kgy)
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Dye-Decolourising Peroxidase Dtpb (112 Kgy) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe402
b:21.8
occ:1.00
|
FE
|
F:HEM402
|
0.0
|
21.8
|
1.0
|
|
ND
|
F:HEM402
|
1.9
|
20.5
|
1.0
|
|
NA
|
F:HEM402
|
2.0
|
21.0
|
1.0
|
|
NB
|
F:HEM402
|
2.0
|
25.1
|
1.0
|
|
O
|
F:O401
|
2.0
|
23.6
|
0.7
|
|
NC
|
F:HEM402
|
2.1
|
18.9
|
1.0
|
|
NE2
|
F:HIS225
|
2.1
|
22.1
|
1.0
|
|
C4D
|
F:HEM402
|
2.9
|
20.7
|
1.0
|
|
C1D
|
F:HEM402
|
2.9
|
19.1
|
1.0
|
|
C1A
|
F:HEM402
|
3.0
|
20.0
|
1.0
|
|
C4A
|
F:HEM402
|
3.0
|
21.4
|
1.0
|
|
C4C
|
F:HEM402
|
3.0
|
18.3
|
1.0
|
|
C4B
|
F:HEM402
|
3.0
|
22.4
|
1.0
|
|
C1B
|
F:HEM402
|
3.0
|
23.6
|
1.0
|
|
CE1
|
F:HIS225
|
3.1
|
24.8
|
1.0
|
|
C1C
|
F:HEM402
|
3.1
|
20.0
|
1.0
|
|
CD2
|
F:HIS225
|
3.2
|
23.1
|
1.0
|
|
CHD
|
F:HEM402
|
3.3
|
19.4
|
1.0
|
|
CHA
|
F:HEM402
|
3.3
|
20.6
|
1.0
|
|
CHB
|
F:HEM402
|
3.4
|
20.6
|
1.0
|
|
CHC
|
F:HEM402
|
3.4
|
21.0
|
1.0
|
|
NH1
|
F:ARG243
|
4.0
|
23.1
|
1.0
|
|
C3D
|
F:HEM402
|
4.1
|
20.7
|
1.0
|
|
C2D
|
F:HEM402
|
4.2
|
20.6
|
1.0
|
|
C2A
|
F:HEM402
|
4.2
|
19.9
|
1.0
|
|
C3A
|
F:HEM402
|
4.2
|
19.8
|
1.0
|
|
ND1
|
F:HIS225
|
4.2
|
23.0
|
1.0
|
|
C2B
|
F:HEM402
|
4.3
|
22.6
|
1.0
|
|
C3B
|
F:HEM402
|
4.3
|
23.8
|
1.0
|
|
CG
|
F:HIS225
|
4.3
|
21.2
|
1.0
|
|
C3C
|
F:HEM402
|
4.3
|
21.4
|
1.0
|
|
C2C
|
F:HEM402
|
4.3
|
21.0
|
1.0
|
|
ND2
|
F:ASN245
|
4.5
|
31.7
|
1.0
|
|
CD
|
F:ARG243
|
4.5
|
22.4
|
1.0
|
|
CZ
|
F:ARG243
|
4.7
|
22.7
|
1.0
|
|
NE
|
F:ARG243
|
4.9
|
22.7
|
1.0
|
|
Reference:
M.Lucic,
J.A.R.Worrall,
M.A.Hough,
R.L.Owen,
R.W.Strange.
Dye-Decolourising Peroxidase Dtpb (56 Kgy) To Be Published.
Page generated: Thu Aug 7 20:12:41 2025
|
