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Iron in PDB 6yr4: Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure

Protein crystallography data

The structure of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure, PDB code: 6yr4 was solved by M.Lucic, F.S.N.Dworkowski, 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) 47.61 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.35, 119.91, 194.15, 90, 90, 90
R / Rfree (%) 18.8 / 23.2

Other elements in 6yr4:

The structure of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure (pdb code 6yr4). 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-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure, PDB code: 6yr4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6yr4

Go back to Iron Binding Sites List in 6yr4
Iron binding site 1 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.5
occ:1.00
 FE A:HEM401 0.0 18.5 1.0
O A:O403 1.7 17.5 1.0
ND A:HEM401 1.9 18.1 1.0
NA A:HEM401 2.0 19.4 1.0
NC A:HEM401 2.1 17.7 1.0
NB A:HEM401 2.1 18.3 1.0
NE2 A:HIS225 2.1 21.2 1.0
C1D A:HEM401 2.9 18.5 1.0
C4D A:HEM401 2.9 19.1 1.0
CD2 A:HIS225 3.0 20.9 1.0
C1A A:HEM401 3.0 18.3 1.0
C1B A:HEM401 3.0 18.2 1.0
C4A A:HEM401 3.0 18.8 1.0
C4C A:HEM401 3.0 18.4 1.0
C4B A:HEM401 3.1 20.6 1.0
C1C A:HEM401 3.1 18.6 1.0
CE1 A:HIS225 3.2 18.3 1.0
CHB A:HEM401 3.4 17.6 1.0
CHA A:HEM401 3.4 18.6 1.0
CHD A:HEM401 3.4 17.9 1.0
CHC A:HEM401 3.5 18.0 1.0
NH1 A:ARG243 3.9 19.0 1.0
CG A:HIS225 4.2 19.0 1.0
C2A A:HEM401 4.2 19.7 1.0
C2D A:HEM401 4.2 19.3 1.0
C3A A:HEM401 4.2 19.9 1.0
C3D A:HEM401 4.2 20.0 1.0
ND1 A:HIS225 4.2 19.7 1.0
C2B A:HEM401 4.2 19.3 1.0
ND2 A:ASN245 4.3 22.6 1.0
C3C A:HEM401 4.3 19.8 1.0
C2C A:HEM401 4.3 18.5 1.0
C3B A:HEM401 4.3 21.6 1.0
CD A:ARG243 4.5 19.2 1.0
CZ A:ARG243 4.7 20.2 1.0
NE A:ARG243 4.8 19.0 1.0

Iron binding site 2 out of 6 in 6yr4

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Iron binding site 2 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:20.4
occ:1.00
 FE B:HEM401 0.0 20.4 1.0
O B:O402 1.8 24.3 1.0
ND B:HEM401 1.9 18.4 1.0
NA B:HEM401 2.0 18.5 1.0
NB B:HEM401 2.1 19.3 1.0
NC B:HEM401 2.1 19.3 1.0
NE2 B:HIS225 2.2 18.8 1.0
C1D B:HEM401 2.9 18.2 1.0
C4D B:HEM401 2.9 18.6 1.0
C4B B:HEM401 3.0 19.3 1.0
C1A B:HEM401 3.0 19.2 1.0
C4C B:HEM401 3.1 19.0 1.0
C1B B:HEM401 3.1 19.8 1.0
C1C B:HEM401 3.1 18.9 1.0
C4A B:HEM401 3.1 20.1 1.0
CE1 B:HIS225 3.1 20.9 1.0
CD2 B:HIS225 3.2 20.1 1.0
CHA B:HEM401 3.4 19.7 1.0
CHD B:HEM401 3.4 18.6 1.0
CHC B:HEM401 3.4 18.5 1.0
CHB B:HEM401 3.5 19.1 1.0
NH1 B:ARG243 3.9 25.9 1.0
C2D B:HEM401 4.1 18.4 1.0
C3D B:HEM401 4.2 19.3 1.0
ND2 B:ASN245 4.2 26.9 1.0
ND1 B:HIS225 4.2 21.6 1.0
C2A B:HEM401 4.2 19.0 1.0
C3A B:HEM401 4.3 18.7 1.0
CD B:ARG243 4.3 23.6 1.0
C2C B:HEM401 4.3 19.5 1.0
C3B B:HEM401 4.3 20.5 1.0
C3C B:HEM401 4.3 19.1 1.0
C2B B:HEM401 4.3 20.1 1.0
CG B:HIS225 4.3 18.8 1.0
CZ B:ARG243 4.7 24.6 1.0
NE B:ARG243 4.8 23.4 1.0

Iron binding site 3 out of 6 in 6yr4

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Iron binding site 3 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:21.1
occ:1.00
 FE C:HEM401 0.0 21.1 1.0
O C:O403 1.7 20.1 1.0
ND C:HEM401 1.9 20.9 1.0
NA C:HEM401 2.0 22.5 1.0
NC C:HEM401 2.1 18.4 1.0
NB C:HEM401 2.1 20.5 1.0
NE2 C:HIS225 2.1 20.4 1.0
C1D C:HEM401 2.9 19.4 1.0
C4D C:HEM401 2.9 18.7 1.0
C1A C:HEM401 3.0 19.1 1.0
C4A C:HEM401 3.0 21.0 1.0
C4C C:HEM401 3.0 19.4 1.0
CD2 C:HIS225 3.0 23.3 1.0
C1B C:HEM401 3.0 21.6 1.0
C4B C:HEM401 3.1 20.9 1.0
C1C C:HEM401 3.1 19.1 1.0
CE1 C:HIS225 3.2 22.2 1.0
CHA C:HEM401 3.4 19.8 1.0
CHD C:HEM401 3.4 18.1 1.0
CHB C:HEM401 3.4 20.7 1.0
CHC C:HEM401 3.5 18.2 1.0
NH1 C:ARG243 3.9 21.6 1.0
C2A C:HEM401 4.2 20.1 1.0
C3A C:HEM401 4.2 19.5 1.0
C2D C:HEM401 4.2 18.9 1.0
CG C:HIS225 4.2 23.1 1.0
C3D C:HEM401 4.2 19.6 1.0
C3C C:HEM401 4.2 18.2 1.0
ND1 C:HIS225 4.2 22.5 1.0
C2B C:HEM401 4.3 20.5 1.0
ND2 C:ASN245 4.3 20.9 1.0
C2C C:HEM401 4.3 18.4 1.0
C3B C:HEM401 4.3 21.6 1.0
CD C:ARG243 4.5 22.8 1.0
CZ C:ARG243 4.7 21.7 1.0
NE C:ARG243 4.9 21.8 1.0

Iron binding site 4 out of 6 in 6yr4

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Iron binding site 4 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:17.1
occ:1.00
 FE D:HEM401 0.0 17.1 1.0
O D:O403 1.8 18.1 1.0
ND D:HEM401 1.9 16.3 1.0
NA D:HEM401 2.0 17.0 1.0
NC D:HEM401 2.0 17.2 1.0
NB D:HEM401 2.0 18.3 1.0
NE2 D:HIS225 2.2 19.6 1.0
C1D D:HEM401 2.9 16.5 1.0
C4D D:HEM401 3.0 16.6 1.0
C4B D:HEM401 3.0 18.0 1.0
C1A D:HEM401 3.0 16.4 1.0
C4C D:HEM401 3.0 17.2 1.0
C1B D:HEM401 3.0 18.7 1.0
C4A D:HEM401 3.0 18.6 1.0
C1C D:HEM401 3.1 17.1 1.0
CD2 D:HIS225 3.1 18.8 1.0
CE1 D:HIS225 3.2 19.8 1.0
CHD D:HEM401 3.4 17.3 1.0
CHC D:HEM401 3.4 16.6 1.0
CHA D:HEM401 3.4 16.4 1.0
CHB D:HEM401 3.4 18.4 1.0
NH1 D:ARG243 3.9 17.4 1.0
C2D D:HEM401 4.2 17.5 1.0
ND2 D:ASN245 4.2 24.8 1.0
C2A D:HEM401 4.2 17.1 1.0
C3D D:HEM401 4.2 17.0 1.0
C3A D:HEM401 4.2 18.2 1.0
C2C D:HEM401 4.2 15.6 1.0
C3C D:HEM401 4.2 16.4 1.0
C3B D:HEM401 4.2 17.8 1.0
C2B D:HEM401 4.2 18.7 1.0
CG D:HIS225 4.3 18.4 1.0
ND1 D:HIS225 4.3 19.9 1.0
CD D:ARG243 4.4 19.9 1.0
CZ D:ARG243 4.6 17.4 1.0
NE D:ARG243 4.8 19.4 1.0

Iron binding site 5 out of 6 in 6yr4

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Iron binding site 5 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:21.7
occ:1.00
 FE E:HEM401 0.0 21.7 1.0
O E:O402 1.8 21.4 1.0
ND E:HEM401 1.9 20.6 1.0
NA E:HEM401 2.0 19.2 1.0
NB E:HEM401 2.1 20.6 1.0
NC E:HEM401 2.1 21.6 1.0
NE2 E:HIS225 2.1 20.3 1.0
C1D E:HEM401 2.9 22.6 1.0
C4D E:HEM401 2.9 21.3 1.0
C4C E:HEM401 3.0 20.0 1.0
C1B E:HEM401 3.0 21.0 1.0
C4B E:HEM401 3.0 20.6 1.0
C1A E:HEM401 3.0 20.7 1.0
C4A E:HEM401 3.0 20.7 1.0
CE1 E:HIS225 3.1 22.0 1.0
C1C E:HEM401 3.1 20.2 1.0
CD2 E:HIS225 3.1 20.0 1.0
CHD E:HEM401 3.3 21.4 1.0
CHA E:HEM401 3.4 20.2 1.0
CHB E:HEM401 3.4 18.4 1.0
CHC E:HEM401 3.5 21.0 1.0
NH1 E:ARG243 3.9 23.6 1.0
ND2 E:ASN245 4.2 25.4 1.0
C2D E:HEM401 4.2 21.8 1.0
C3D E:HEM401 4.2 21.2 1.0
ND1 E:HIS225 4.2 20.4 1.0
C2B E:HEM401 4.2 21.0 1.0
C3A E:HEM401 4.2 20.4 1.0
C3B E:HEM401 4.2 23.0 1.0
CG E:HIS225 4.2 21.2 1.0
C3C E:HEM401 4.2 20.3 1.0
C2A E:HEM401 4.3 20.9 1.0
C2C E:HEM401 4.3 21.8 1.0
CD E:ARG243 4.4 21.9 1.0
CZ E:ARG243 4.7 22.3 1.0
NE E:ARG243 4.9 23.0 1.0

Iron binding site 6 out of 6 in 6yr4

Go back to Iron Binding Sites List in 6yr4
Iron binding site 6 out of 6 in the Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Dye-Type Peroxidase Dtpb in the Ferryl State: Spectroscopically Validated Composite Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:20.3
occ:1.00
 FE F:HEM401 0.0 20.3 1.0
O F:O402 1.7 20.6 1.0
ND F:HEM401 1.9 19.9 1.0
NA F:HEM401 2.0 18.4 1.0
NB F:HEM401 2.1 18.6 1.0
NE2 F:HIS225 2.1 18.6 1.0
NC F:HEM401 2.1 20.2 1.0
C1D F:HEM401 2.9 20.5 1.0
C4D F:HEM401 2.9 20.1 1.0
C1A F:HEM401 3.0 20.0 1.0
C4B F:HEM401 3.0 20.1 1.0
CE1 F:HIS225 3.0 21.6 1.0
C4A F:HEM401 3.0 19.6 1.0
C1B F:HEM401 3.1 19.4 1.0
CD2 F:HIS225 3.1 20.7 1.0
C4C F:HEM401 3.1 20.3 1.0
C1C F:HEM401 3.1 19.6 1.0
CHA F:HEM401 3.3 20.2 1.0
CHD F:HEM401 3.4 19.1 1.0
CHC F:HEM401 3.4 17.8 1.0
CHB F:HEM401 3.5 17.8 1.0
NH1 F:ARG243 3.9 21.6 1.0
ND1 F:HIS225 4.1 20.2 1.0
CG F:HIS225 4.2 20.0 1.0
C2D F:HEM401 4.2 19.8 1.0
C2A F:HEM401 4.2 18.2 1.0
C3D F:HEM401 4.2 20.1 1.0
C3A F:HEM401 4.2 18.7 1.0
C3B F:HEM401 4.3 18.7 1.0
C2B F:HEM401 4.3 18.2 1.0
ND2 F:ASN245 4.3 22.1 1.0
C3C F:HEM401 4.3 20.1 1.0
C2C F:HEM401 4.3 20.1 1.0
CD F:ARG243 4.4 20.9 1.0
CZ F:ARG243 4.7 22.0 1.0
NE F:ARG243 4.9 20.6 1.0

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 16:41:49 2024

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