Iron in PDB 7odz: Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with An Activated Form of Oxygen and Veratryl Alcohol

The structure of Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with An Activated Form of Oxygen and Veratryl Alcohol, PDB code: 7odz was solved by A.Rai, R.Fedorov, D.J.Manstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.11 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	140.44, 140.44, 95.28, 90, 90, 90
R / Rfree (%)	15.1 / 16.8

The binding sites of Iron atom in the Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with An Activated Form of Oxygen and Veratryl Alcohol (pdb code 7odz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with An Activated Form of Oxygen and Veratryl Alcohol, PDB code: 7odz:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with An Activated Form of Oxygen and Veratryl Alcohol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with An Activated Form of Oxygen and Veratryl Alcohol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:18.9 occ:1.00 FE A:HEM401 0.0 18.9 1.0 ND A:HEM401 1.9 17.1 1.0 NA A:HEM401 2.0 20.5 1.0 NC A:HEM401 2.1 17.7 1.0 NB A:HEM401 2.1 19.9 1.0 NE2 A:HIS222 2.1 18.8 1.0 O1 A:OXY407 2.4 31.0 1.0 C1D A:HEM401 2.9 18.2 1.0 C4D A:HEM401 3.0 17.4 1.0 C1A A:HEM401 3.0 20.3 1.0 C4B A:HEM401 3.0 18.5 1.0 C4C A:HEM401 3.1 19.6 1.0 C4A A:HEM401 3.1 22.9 1.0 C1B A:HEM401 3.1 20.8 1.0 CD2 A:HIS222 3.1 18.4 1.0 C1C A:HEM401 3.1 17.8 1.0 CE1 A:HIS222 3.1 21.2 1.0 CHD A:HEM401 3.4 18.8 1.0 CHA A:HEM401 3.4 18.9 1.0 CHC A:HEM401 3.5 18.4 1.0 CHB A:HEM401 3.5 21.7 1.0 NH1 A:ARG239 4.1 22.1 1.0 C2D A:HEM401 4.2 19.5 1.0 C3D A:HEM401 4.2 18.9 1.0 C2A A:HEM401 4.2 18.7 1.0 ND1 A:HIS222 4.2 19.3 1.0 C3A A:HEM401 4.2 21.0 1.0 CG A:HIS222 4.2 18.3 1.0 C3C A:HEM401 4.3 18.4 1.0 C2C A:HEM401 4.3 16.6 1.0 C2B A:HEM401 4.3 19.8 1.0 C3B A:HEM401 4.3 19.1 1.0 O2 A:OXY407 4.4 28.9 1.0 CD A:ARG239 4.7 19.1 1.0 OD1 A:ASP149 4.7 34.6 1.0 CE1 A:PHE255 4.8 18.0 1.0 CZ A:ARG239 4.8 18.6 1.0

Iron binding site 2 out of 2 in the Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with An Activated Form of Oxygen and Veratryl Alcohol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dictyostelium Discoideum Dye Decolorizing Peroxidase Dypa in Complex with An Activated Form of Oxygen and Veratryl Alcohol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:19.7 occ:1.00 FE B:HEM401 0.0 19.7 1.0 ND B:HEM401 1.9 19.2 1.0 NA B:HEM401 2.0 19.6 1.0 NC B:HEM401 2.1 19.4 1.0 NB B:HEM401 2.1 22.3 1.0 NE2 B:HIS222 2.1 17.3 1.0 O1 B:OXY404 2.3 26.4 1.0 C1D B:HEM401 2.9 17.3 1.0 C4D B:HEM401 3.0 17.1 1.0 C1A B:HEM401 3.0 18.0 1.0 C4B B:HEM401 3.0 19.0 1.0 C4C B:HEM401 3.0 19.7 1.0 C4A B:HEM401 3.1 19.9 1.0 CD2 B:HIS222 3.1 19.0 1.0 C1C B:HEM401 3.1 20.1 1.0 C1B B:HEM401 3.1 20.3 1.0 CE1 B:HIS222 3.1 22.1 1.0 CHD B:HEM401 3.4 18.8 1.0 CHA B:HEM401 3.4 17.4 1.0 CHC B:HEM401 3.4 19.4 1.0 CHB B:HEM401 3.5 20.6 1.0 NH1 B:ARG239 4.1 21.9 1.0 O2 B:OXY404 4.2 27.0 1.0 C2D B:HEM401 4.2 20.4 1.0 ND1 B:HIS222 4.2 22.6 1.0 CG B:HIS222 4.2 20.1 1.0 C3D B:HEM401 4.2 20.1 1.0 C2A B:HEM401 4.2 19.8 1.0 C3A B:HEM401 4.2 20.4 1.0 C3C B:HEM401 4.3 19.4 1.0 C2C B:HEM401 4.3 17.7 1.0 C2B B:HEM401 4.3 22.0 1.0 C3B B:HEM401 4.3 20.9 1.0 CD B:ARG239 4.7 19.1 1.0 CE1 B:PHE255 4.8 18.4 1.0 OD1 B:ASP149 4.8 41.7 1.0 CZ B:ARG239 4.8 19.7 1.0

A.Rai, J.P.Klare, P.Y.A.Reinke, F.Englmaier, J.Fohrer, R.Fedorov, M.H.Taft, I.Chizhov, U.Curth, O.Plettenburg, D.J.Manstein. Structural and Biochemical Characterization of A Dye-Decolorizing Peroxidase From Dictyostelium Discoideum . Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 34200865
DOI: 10.3390/IJMS22126265