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Iron in PDB 6yrd: Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State
Protein crystallography data
The structure of Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State, PDB code: 6yrd
was solved by
M.Lucic,
D.A.Axford,
R.L.Owen,
J.A.R.Worrall,
M.A.Hough,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
| Resolution Low / High (Å) | 13.00 / 1.75 |
| Space group | P 21 21 21 |
| Cell size a, b, c (Å), α, β, γ (°) | 86.3, 120, 198.45, 90, 90, 90 |
| R / Rfree (%) | 16.7 / 19.9 |
Other elements in 6yrd:
The structure of Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State also contains other interesting chemical elements:
| Magnesium | (Mg) | 2 atoms |
Iron Binding Sites:
The binding sites of Iron atom in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State
(pdb code 6yrd). 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 in the Ferryl State, PDB code: 6yrd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;
In total 6 binding sites of Iron where determined in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State, PDB code: 6yrd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;
Iron binding site 1 out of 6 in 6yrd
Go back to
Iron Binding Sites List in 6yrd
Iron binding site 1 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State
Mono view
Stereo pair view
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 in the Ferryl State within 5.0Å range:
|
Iron binding site 2 out of 6 in 6yrd
Go back to
Iron Binding Sites List in 6yrd
Iron binding site 2 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State
Mono view
Stereo pair view
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 in the Ferryl State within 5.0Å range:
|
Iron binding site 3 out of 6 in 6yrd
Go back to
Iron Binding Sites List in 6yrd
Iron binding site 3 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State
Mono view
Stereo pair view
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 in the Ferryl State within 5.0Å range:
|
Iron binding site 4 out of 6 in 6yrd
Go back to
Iron Binding Sites List in 6yrd
Iron binding site 4 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State
Mono view
Stereo pair view
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 in the Ferryl State within 5.0Å range:
|
Iron binding site 5 out of 6 in 6yrd
Go back to
Iron Binding Sites List in 6yrd
Iron binding site 5 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State
Mono view
Stereo pair view
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 in the Ferryl State within 5.0Å range:
|
Iron binding site 6 out of 6 in 6yrd
Go back to
Iron Binding Sites List in 6yrd
Iron binding site 6 out
of 6 in the Sfx Structure of Dye-Type Peroxidase Dtpb in the Ferryl State
Mono view
Stereo pair view
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 in the Ferryl State within 5.0Å range:
|
Reference:
M.Lucic,
D.A.Svistunenko,
M.T.Wilson,
A.K.Chaplin,
B.Davy,
A.Ebrahim,
D.Axford,
T.Tosha,
H.Sugimoto,
S.Owada,
F.S.N.Dworkowski,
I.Tews,
R.L.Owen,
M.A.Hough,
J.A.R.Worrall.
Serial Femtosecond Zero Dose Crystallography Captures A Water-Free Distal Heme Site in A Dye-Decolorising Peroxidase to Reveal A Catalytic Role For An Arginine in Fe IV =O Formation. Angew.Chem.Int.Ed.Engl. V. 59 21656 2020.
ISSN: ESSN 1521-3773
PubMed: 32780931
DOI: 10.1002/ANIE.202008622
Page generated: Wed Aug 7 16:43:11 2024
ISSN: ESSN 1521-3773
PubMed: 32780931
DOI: 10.1002/ANIE.202008622
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