Iron in PDB 7zmj: Sfx Structure of Dye-Type Peroxidase Dtpb R243A Variant in the Ferric State

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

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

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 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 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 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 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 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 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

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