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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:

Magnesium (Mg) 2 atoms

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

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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

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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

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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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