Iron in PDB 7o9l: Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with Cyanide.
Protein crystallography data
The structure of Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with Cyanide., PDB code: 7o9l
was solved by
A.Rai,
R.Fedorov,
D.J.Manstein,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.22 /
1.85
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
141.05,
141.05,
95.48,
90,
90,
90
|
R / Rfree (%)
|
15.5 /
18
|
Iron Binding Sites:
The binding sites of Iron atom in the Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with Cyanide.
(pdb code 7o9l). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the
Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with Cyanide., PDB code: 7o9l:
Jump to Iron binding site number:
1;
2;
Iron binding site 1 out
of 2 in 7o9l
Go back to
Iron Binding Sites List in 7o9l
Iron binding site 1 out
of 2 in the Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with Cyanide.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with Cyanide. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1001
b:21.6
occ:1.00
|
FE
|
A:HEM1001
|
0.0
|
21.6
|
1.0
|
ND
|
A:HEM1001
|
1.9
|
19.7
|
1.0
|
NA
|
A:HEM1001
|
2.0
|
20.8
|
1.0
|
NC
|
A:HEM1001
|
2.1
|
20.1
|
1.0
|
NB
|
A:HEM1001
|
2.1
|
20.6
|
1.0
|
NE2
|
A:HIS222
|
2.2
|
24.2
|
1.0
|
C1D
|
A:HEM1001
|
2.9
|
20.4
|
1.0
|
C
|
A:CYN1006
|
2.9
|
30.4
|
1.0
|
C4D
|
A:HEM1001
|
2.9
|
21.7
|
1.0
|
C1A
|
A:HEM1001
|
3.0
|
23.6
|
1.0
|
C4B
|
A:HEM1001
|
3.0
|
21.1
|
1.0
|
C4C
|
A:HEM1001
|
3.0
|
22.7
|
1.0
|
C4A
|
A:HEM1001
|
3.0
|
20.6
|
1.0
|
C1B
|
A:HEM1001
|
3.1
|
23.7
|
1.0
|
C1C
|
A:HEM1001
|
3.1
|
23.0
|
1.0
|
CD2
|
A:HIS222
|
3.1
|
23.3
|
1.0
|
CE1
|
A:HIS222
|
3.2
|
27.2
|
1.0
|
CHD
|
A:HEM1001
|
3.4
|
21.5
|
1.0
|
CHA
|
A:HEM1001
|
3.4
|
21.5
|
1.0
|
CHC
|
A:HEM1001
|
3.5
|
21.3
|
1.0
|
CHB
|
A:HEM1001
|
3.5
|
23.7
|
1.0
|
NH1
|
A:ARG239
|
4.2
|
23.3
|
1.0
|
C2D
|
A:HEM1001
|
4.2
|
21.1
|
1.0
|
C3D
|
A:HEM1001
|
4.2
|
22.6
|
1.0
|
C2A
|
A:HEM1001
|
4.2
|
19.4
|
1.0
|
C3A
|
A:HEM1001
|
4.2
|
22.8
|
1.0
|
C3C
|
A:HEM1001
|
4.3
|
20.2
|
1.0
|
N
|
A:CYN1006
|
4.3
|
28.8
|
1.0
|
C2C
|
A:HEM1001
|
4.3
|
21.8
|
1.0
|
ND1
|
A:HIS222
|
4.3
|
23.9
|
1.0
|
CG
|
A:HIS222
|
4.3
|
23.6
|
1.0
|
C3B
|
A:HEM1001
|
4.3
|
19.6
|
1.0
|
C2B
|
A:HEM1001
|
4.3
|
23.1
|
1.0
|
CD
|
A:ARG239
|
4.7
|
22.5
|
1.0
|
OD1
|
A:ASP149
|
4.8
|
57.9
|
1.0
|
CE1
|
A:PHE255
|
4.8
|
21.7
|
1.0
|
CZ
|
A:ARG239
|
4.8
|
25.4
|
1.0
|
|
Iron binding site 2 out
of 2 in 7o9l
Go back to
Iron Binding Sites List in 7o9l
Iron binding site 2 out
of 2 in the Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with Cyanide.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with Cyanide. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1001
b:23.2
occ:1.00
|
FE
|
B:HEM1001
|
0.0
|
23.2
|
1.0
|
ND
|
B:HEM1001
|
1.9
|
21.2
|
1.0
|
NA
|
B:HEM1001
|
2.0
|
20.0
|
1.0
|
NC
|
B:HEM1001
|
2.1
|
20.8
|
1.0
|
NB
|
B:HEM1001
|
2.1
|
21.8
|
1.0
|
NE2
|
B:HIS222
|
2.2
|
25.3
|
1.0
|
C1D
|
B:HEM1001
|
2.9
|
21.6
|
1.0
|
C
|
B:CYN1005
|
2.9
|
30.6
|
1.0
|
C4D
|
B:HEM1001
|
3.0
|
23.9
|
1.0
|
C1A
|
B:HEM1001
|
3.0
|
21.5
|
1.0
|
C4B
|
B:HEM1001
|
3.0
|
22.6
|
1.0
|
C4C
|
B:HEM1001
|
3.0
|
24.1
|
1.0
|
C4A
|
B:HEM1001
|
3.1
|
21.1
|
1.0
|
C1C
|
B:HEM1001
|
3.1
|
23.3
|
1.0
|
C1B
|
B:HEM1001
|
3.1
|
25.5
|
1.0
|
CD2
|
B:HIS222
|
3.1
|
23.5
|
1.0
|
CE1
|
B:HIS222
|
3.2
|
28.2
|
1.0
|
CHD
|
B:HEM1001
|
3.4
|
24.2
|
1.0
|
CHA
|
B:HEM1001
|
3.4
|
22.6
|
1.0
|
CHC
|
B:HEM1001
|
3.4
|
21.9
|
1.0
|
CHB
|
B:HEM1001
|
3.5
|
22.2
|
1.0
|
NH2
|
B:ARG239
|
4.1
|
24.9
|
1.0
|
C2D
|
B:HEM1001
|
4.2
|
24.2
|
1.0
|
C3D
|
B:HEM1001
|
4.2
|
24.7
|
1.0
|
C2A
|
B:HEM1001
|
4.2
|
20.7
|
1.0
|
C3C
|
B:HEM1001
|
4.2
|
24.0
|
1.0
|
C3A
|
B:HEM1001
|
4.2
|
21.6
|
1.0
|
N
|
B:CYN1005
|
4.3
|
28.0
|
1.0
|
ND1
|
B:HIS222
|
4.3
|
24.8
|
1.0
|
C2C
|
B:HEM1001
|
4.3
|
22.3
|
1.0
|
CG
|
B:HIS222
|
4.3
|
23.2
|
1.0
|
C3B
|
B:HEM1001
|
4.3
|
21.1
|
1.0
|
C2B
|
B:HEM1001
|
4.3
|
22.4
|
1.0
|
CD
|
B:ARG239
|
4.7
|
22.8
|
1.0
|
CZ
|
B:ARG239
|
4.8
|
26.6
|
1.0
|
CE1
|
B:PHE255
|
4.8
|
21.3
|
1.0
|
OD1
|
B:ASP149
|
5.0
|
54.1
|
1.0
|
|
Reference:
A.Rai,
J.P.Klare,
P.Y.A.Reinke,
F.Englmaier,
J.Fohrer,
R.Fedorov,
M.H.Taft,
I.Chizhov,
U.Curth,
O.Plettenburg,
D.J.Manstein.
Structural and Biochemical Characterization of A Dye-Decolorizing Peroxidase From Dictyostelium Discoideum . Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 34200865
DOI: 10.3390/IJMS22126265
Page generated: Sat Aug 21 14:21:34 2021
|