Iron in PDB 7zmj: Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State
Protein crystallography data
The structure of Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State, PDB code: 7zmj
was solved by
M.Lucic,
J.A.R.Worrall,
M.A.Hough,
A.Shilova,
D.A.Axford,
R.L.Owen,
T.Tosha,
H.Sugimoto,
S.Owada,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.27 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.6,
121.3,
197.6,
90,
90,
90
|
R / Rfree (%)
|
20.2 /
23
|
Other elements in 7zmj:
The structure of Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State
(pdb code 7zmj). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State, PDB code: 7zmj:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 7zmj
Go back to
Iron Binding Sites List in 7zmj
Iron binding site 1 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:19.2
occ:1.00
|
FE
|
A:HEM401
|
0.0
|
19.2
|
1.0
|
ND
|
A:HEM401
|
1.9
|
18.2
|
1.0
|
NA
|
A:HEM401
|
2.0
|
17.8
|
1.0
|
NB
|
A:HEM401
|
2.1
|
18.1
|
1.0
|
NC
|
A:HEM401
|
2.1
|
18.4
|
1.0
|
NE2
|
A:HIS225
|
2.2
|
19.4
|
1.0
|
O
|
A:HOH591
|
2.2
|
20.1
|
1.0
|
C1D
|
A:HEM401
|
2.9
|
21.0
|
1.0
|
C1B
|
A:HEM401
|
3.0
|
17.6
|
1.0
|
C4D
|
A:HEM401
|
3.0
|
20.4
|
1.0
|
C4A
|
A:HEM401
|
3.0
|
18.4
|
1.0
|
C1A
|
A:HEM401
|
3.1
|
19.0
|
1.0
|
C4C
|
A:HEM401
|
3.1
|
18.5
|
1.0
|
C4B
|
A:HEM401
|
3.1
|
20.2
|
1.0
|
CE1
|
A:HIS225
|
3.1
|
18.4
|
1.0
|
C1C
|
A:HEM401
|
3.2
|
17.8
|
1.0
|
CD2
|
A:HIS225
|
3.2
|
17.4
|
1.0
|
CHB
|
A:HEM401
|
3.4
|
18.3
|
1.0
|
CHD
|
A:HEM401
|
3.4
|
20.9
|
1.0
|
CHA
|
A:HEM401
|
3.5
|
20.8
|
1.0
|
CHC
|
A:HEM401
|
3.5
|
20.0
|
1.0
|
O
|
A:HOH555
|
4.0
|
21.0
|
1.0
|
C2D
|
A:HEM401
|
4.2
|
23.6
|
1.0
|
C2B
|
A:HEM401
|
4.2
|
19.3
|
1.0
|
C3A
|
A:HEM401
|
4.2
|
22.2
|
1.0
|
ND1
|
A:HIS225
|
4.2
|
19.1
|
1.0
|
C3D
|
A:HEM401
|
4.2
|
21.0
|
1.0
|
C2A
|
A:HEM401
|
4.3
|
19.2
|
1.0
|
CG
|
A:HIS225
|
4.3
|
18.7
|
1.0
|
C3B
|
A:HEM401
|
4.3
|
18.7
|
1.0
|
C3C
|
A:HEM401
|
4.3
|
19.4
|
1.0
|
C2C
|
A:HEM401
|
4.4
|
17.1
|
1.0
|
ND2
|
A:ASN245
|
4.5
|
37.2
|
1.0
|
|
Iron binding site 2 out
of 6 in 7zmj
Go back to
Iron Binding Sites List in 7zmj
Iron binding site 2 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:21.0
occ:1.00
|
FE
|
B:HEM401
|
0.0
|
21.0
|
1.0
|
ND
|
B:HEM401
|
1.9
|
22.0
|
1.0
|
NA
|
B:HEM401
|
2.0
|
20.9
|
1.0
|
NB
|
B:HEM401
|
2.1
|
19.6
|
1.0
|
NC
|
B:HEM401
|
2.1
|
20.1
|
1.0
|
NE2
|
B:HIS225
|
2.2
|
20.0
|
1.0
|
O
|
B:HOH585
|
2.3
|
23.0
|
1.0
|
C1D
|
B:HEM401
|
2.9
|
22.6
|
1.0
|
C4D
|
B:HEM401
|
3.0
|
19.3
|
1.0
|
C1B
|
B:HEM401
|
3.0
|
18.5
|
1.0
|
C4C
|
B:HEM401
|
3.0
|
20.8
|
1.0
|
C4A
|
B:HEM401
|
3.1
|
19.9
|
1.0
|
C4B
|
B:HEM401
|
3.1
|
19.0
|
1.0
|
C1A
|
B:HEM401
|
3.1
|
19.4
|
1.0
|
CD2
|
B:HIS225
|
3.1
|
19.5
|
1.0
|
C1C
|
B:HEM401
|
3.1
|
18.8
|
1.0
|
CE1
|
B:HIS225
|
3.2
|
20.6
|
1.0
|
CHB
|
B:HEM401
|
3.4
|
19.0
|
1.0
|
CHD
|
B:HEM401
|
3.4
|
21.3
|
1.0
|
CHA
|
B:HEM401
|
3.5
|
20.8
|
1.0
|
CHC
|
B:HEM401
|
3.5
|
18.8
|
1.0
|
C2D
|
B:HEM401
|
4.2
|
23.1
|
1.0
|
O
|
B:HOH535
|
4.2
|
33.1
|
1.0
|
C3D
|
B:HEM401
|
4.2
|
22.3
|
1.0
|
C2B
|
B:HEM401
|
4.2
|
19.4
|
1.0
|
ND1
|
B:HIS225
|
4.3
|
19.9
|
1.0
|
C2A
|
B:HEM401
|
4.3
|
20.6
|
1.0
|
CG
|
B:HIS225
|
4.3
|
19.0
|
1.0
|
C3C
|
B:HEM401
|
4.3
|
19.7
|
1.0
|
C3A
|
B:HEM401
|
4.3
|
20.5
|
1.0
|
C3B
|
B:HEM401
|
4.3
|
19.3
|
1.0
|
C2C
|
B:HEM401
|
4.3
|
19.8
|
1.0
|
ND2
|
B:ASN245
|
4.3
|
35.6
|
1.0
|
|
Iron binding site 3 out
of 6 in 7zmj
Go back to
Iron Binding Sites List in 7zmj
Iron binding site 3 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:22.2
occ:1.00
|
FE
|
C:HEM401
|
0.0
|
22.2
|
1.0
|
ND
|
C:HEM401
|
1.9
|
20.8
|
1.0
|
NA
|
C:HEM401
|
2.0
|
18.5
|
1.0
|
NB
|
C:HEM401
|
2.1
|
19.9
|
1.0
|
NC
|
C:HEM401
|
2.1
|
19.9
|
1.0
|
NE2
|
C:HIS225
|
2.2
|
21.2
|
1.0
|
O
|
C:HOH613
|
2.3
|
17.1
|
1.0
|
C4D
|
C:HEM401
|
3.0
|
19.4
|
1.0
|
C1D
|
C:HEM401
|
3.0
|
20.4
|
1.0
|
C4A
|
C:HEM401
|
3.0
|
20.6
|
1.0
|
C4C
|
C:HEM401
|
3.0
|
22.0
|
1.0
|
C1B
|
C:HEM401
|
3.0
|
22.8
|
1.0
|
C1A
|
C:HEM401
|
3.0
|
19.6
|
1.0
|
C4B
|
C:HEM401
|
3.1
|
20.2
|
1.0
|
CD2
|
C:HIS225
|
3.1
|
21.2
|
1.0
|
C1C
|
C:HEM401
|
3.1
|
19.4
|
1.0
|
CE1
|
C:HIS225
|
3.1
|
22.6
|
1.0
|
CHD
|
C:HEM401
|
3.4
|
21.6
|
1.0
|
CHB
|
C:HEM401
|
3.4
|
21.6
|
1.0
|
CHA
|
C:HEM401
|
3.4
|
19.6
|
1.0
|
CHC
|
C:HEM401
|
3.5
|
18.8
|
1.0
|
O
|
C:HOH552
|
4.1
|
27.4
|
1.0
|
C3D
|
C:HEM401
|
4.2
|
23.4
|
1.0
|
C2D
|
C:HEM401
|
4.2
|
23.4
|
1.0
|
C3A
|
C:HEM401
|
4.2
|
21.5
|
1.0
|
ND1
|
C:HIS225
|
4.2
|
20.3
|
1.0
|
C2A
|
C:HEM401
|
4.3
|
20.5
|
1.0
|
CG
|
C:HIS225
|
4.3
|
20.2
|
1.0
|
C2B
|
C:HEM401
|
4.3
|
19.8
|
1.0
|
C3B
|
C:HEM401
|
4.3
|
19.3
|
1.0
|
C3C
|
C:HEM401
|
4.3
|
19.1
|
1.0
|
C2C
|
C:HEM401
|
4.3
|
18.9
|
1.0
|
ND2
|
C:ASN245
|
4.5
|
32.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 7zmj
Go back to
Iron Binding Sites List in 7zmj
Iron binding site 4 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:19.8
occ:1.00
|
FE
|
D:HEM401
|
0.0
|
19.8
|
1.0
|
ND
|
D:HEM401
|
1.9
|
19.6
|
1.0
|
NA
|
D:HEM401
|
2.0
|
18.5
|
1.0
|
NC
|
D:HEM401
|
2.1
|
18.4
|
1.0
|
NB
|
D:HEM401
|
2.1
|
19.7
|
1.0
|
NE2
|
D:HIS225
|
2.1
|
18.1
|
1.0
|
O
|
D:HOH603
|
2.3
|
22.2
|
1.0
|
C1D
|
D:HEM401
|
2.9
|
19.5
|
1.0
|
C4D
|
D:HEM401
|
3.0
|
20.0
|
1.0
|
C4C
|
D:HEM401
|
3.0
|
19.6
|
1.0
|
C1A
|
D:HEM401
|
3.0
|
19.9
|
1.0
|
C4B
|
D:HEM401
|
3.1
|
17.8
|
1.0
|
C4A
|
D:HEM401
|
3.1
|
18.1
|
1.0
|
C1C
|
D:HEM401
|
3.1
|
19.2
|
1.0
|
C1B
|
D:HEM401
|
3.1
|
20.5
|
1.0
|
CD2
|
D:HIS225
|
3.1
|
17.8
|
1.0
|
CE1
|
D:HIS225
|
3.1
|
17.2
|
1.0
|
CHD
|
D:HEM401
|
3.4
|
18.5
|
1.0
|
CHA
|
D:HEM401
|
3.4
|
19.9
|
1.0
|
CHC
|
D:HEM401
|
3.4
|
17.2
|
1.0
|
CHB
|
D:HEM401
|
3.5
|
19.8
|
1.0
|
O
|
D:HOH558
|
4.1
|
25.0
|
1.0
|
C2D
|
D:HEM401
|
4.2
|
21.4
|
1.0
|
ND1
|
D:HIS225
|
4.2
|
17.8
|
1.0
|
C3D
|
D:HEM401
|
4.2
|
21.9
|
1.0
|
CG
|
D:HIS225
|
4.2
|
19.5
|
1.0
|
C2A
|
D:HEM401
|
4.3
|
21.3
|
1.0
|
C3C
|
D:HEM401
|
4.3
|
19.9
|
1.0
|
C2C
|
D:HEM401
|
4.3
|
18.1
|
1.0
|
C3A
|
D:HEM401
|
4.3
|
19.2
|
1.0
|
C2B
|
D:HEM401
|
4.4
|
20.1
|
1.0
|
C3B
|
D:HEM401
|
4.4
|
19.9
|
1.0
|
ND2
|
D:ASN245
|
4.5
|
28.1
|
1.0
|
|
Iron binding site 5 out
of 6 in 7zmj
Go back to
Iron Binding Sites List in 7zmj
Iron binding site 5 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe401
b:21.6
occ:1.00
|
FE
|
E:HEM401
|
0.0
|
21.6
|
1.0
|
ND
|
E:HEM401
|
1.9
|
22.1
|
1.0
|
NA
|
E:HEM401
|
2.0
|
21.1
|
1.0
|
NB
|
E:HEM401
|
2.1
|
20.9
|
1.0
|
NC
|
E:HEM401
|
2.1
|
20.1
|
1.0
|
NE2
|
E:HIS225
|
2.1
|
22.9
|
1.0
|
O
|
E:HOH573
|
2.3
|
20.6
|
1.0
|
C4D
|
E:HEM401
|
2.9
|
23.6
|
1.0
|
C1D
|
E:HEM401
|
3.0
|
22.9
|
1.0
|
C4B
|
E:HEM401
|
3.0
|
22.2
|
1.0
|
C1A
|
E:HEM401
|
3.0
|
21.5
|
1.0
|
C1B
|
E:HEM401
|
3.0
|
21.8
|
1.0
|
C1C
|
E:HEM401
|
3.1
|
19.6
|
1.0
|
CD2
|
E:HIS225
|
3.1
|
22.9
|
1.0
|
C4C
|
E:HEM401
|
3.1
|
20.5
|
1.0
|
C4A
|
E:HEM401
|
3.1
|
23.9
|
1.0
|
CE1
|
E:HIS225
|
3.1
|
24.7
|
1.0
|
CHA
|
E:HEM401
|
3.4
|
23.1
|
1.0
|
CHC
|
E:HEM401
|
3.4
|
19.3
|
1.0
|
CHD
|
E:HEM401
|
3.5
|
20.0
|
1.0
|
CHB
|
E:HEM401
|
3.5
|
20.5
|
1.0
|
O
|
E:HOH555
|
4.0
|
25.0
|
1.0
|
C2D
|
E:HEM401
|
4.2
|
23.8
|
1.0
|
C3D
|
E:HEM401
|
4.2
|
23.6
|
1.0
|
CG
|
E:HIS225
|
4.2
|
23.4
|
1.0
|
ND1
|
E:HIS225
|
4.2
|
22.8
|
1.0
|
C2B
|
E:HEM401
|
4.2
|
21.8
|
1.0
|
C3B
|
E:HEM401
|
4.3
|
21.9
|
1.0
|
C2A
|
E:HEM401
|
4.3
|
21.6
|
1.0
|
C3A
|
E:HEM401
|
4.3
|
22.3
|
1.0
|
C2C
|
E:HEM401
|
4.3
|
18.4
|
1.0
|
C3C
|
E:HEM401
|
4.3
|
20.1
|
1.0
|
ND2
|
E:ASN245
|
4.4
|
40.2
|
1.0
|
|
Iron binding site 6 out
of 6 in 7zmj
Go back to
Iron Binding Sites List in 7zmj
Iron binding site 6 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe401
b:20.6
occ:1.00
|
FE
|
F:HEM401
|
0.0
|
20.6
|
1.0
|
ND
|
F:HEM401
|
1.9
|
21.8
|
1.0
|
NA
|
F:HEM401
|
2.0
|
20.9
|
1.0
|
NB
|
F:HEM401
|
2.1
|
21.3
|
1.0
|
NC
|
F:HEM401
|
2.1
|
21.2
|
1.0
|
NE2
|
F:HIS225
|
2.1
|
20.9
|
1.0
|
O
|
F:HOH586
|
2.3
|
24.1
|
1.0
|
C4D
|
F:HEM401
|
2.9
|
23.7
|
1.0
|
C1D
|
F:HEM401
|
2.9
|
24.3
|
1.0
|
C1A
|
F:HEM401
|
3.0
|
22.3
|
1.0
|
C4C
|
F:HEM401
|
3.0
|
20.6
|
1.0
|
C1B
|
F:HEM401
|
3.0
|
20.4
|
1.0
|
C4B
|
F:HEM401
|
3.1
|
22.3
|
1.0
|
C4A
|
F:HEM401
|
3.1
|
24.0
|
1.0
|
CE1
|
F:HIS225
|
3.1
|
22.6
|
1.0
|
CD2
|
F:HIS225
|
3.1
|
23.6
|
1.0
|
C1C
|
F:HEM401
|
3.1
|
18.8
|
1.0
|
CHD
|
F:HEM401
|
3.4
|
21.5
|
1.0
|
CHA
|
F:HEM401
|
3.4
|
22.5
|
1.0
|
CHB
|
F:HEM401
|
3.5
|
21.8
|
1.0
|
CHC
|
F:HEM401
|
3.5
|
19.9
|
1.0
|
O
|
F:HOH567
|
4.2
|
28.9
|
1.0
|
ND1
|
F:HIS225
|
4.2
|
21.3
|
1.0
|
C2D
|
F:HEM401
|
4.2
|
23.4
|
1.0
|
C3D
|
F:HEM401
|
4.2
|
24.4
|
1.0
|
C2A
|
F:HEM401
|
4.2
|
21.1
|
1.0
|
CG
|
F:HIS225
|
4.2
|
23.0
|
1.0
|
C3A
|
F:HEM401
|
4.3
|
22.2
|
1.0
|
C3C
|
F:HEM401
|
4.3
|
20.8
|
1.0
|
C2B
|
F:HEM401
|
4.3
|
21.3
|
1.0
|
C2C
|
F:HEM401
|
4.3
|
19.9
|
1.0
|
C3B
|
F:HEM401
|
4.3
|
22.0
|
1.0
|
ND2
|
F:ASN245
|
4.5
|
28.8
|
1.0
|
|
Reference:
M.Lucic,
M.T.Wilson,
T.Tosha,
H.Sugimoto,
A.Shilova,
D.Axford,
R.L.Owen,
M.A.Hough,
J.A.R.Worrall.
Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase Dtpb. Acs Catalysis V. 12 13349 2022.
ISSN: ESSN 2155-5435
PubMed: 36366763
DOI: 10.1021/ACSCATAL.2C03754
Page generated: Fri Aug 9 15:04:46 2024
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