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

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

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

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 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 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 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 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 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 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

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