Iron in PDB 2d3q: Crystal Structure of A Decolorizing Peroxidase (Dyp) That Catalyses the Biological Oxidation of Anthraquinone Derivatives

All present enzymatic activity of Crystal Structure of A Decolorizing Peroxidase (Dyp) That Catalyses the Biological Oxidation of Anthraquinone Derivatives:
1.11.1.19;

The structure of Crystal Structure of A Decolorizing Peroxidase (Dyp) That Catalyses the Biological Oxidation of Anthraquinone Derivatives, PDB code: 2d3q was solved by T.Sato, Y.Sugano, M.Shoda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.80
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	136.212, 136.212, 363.596, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 26.7

The binding sites of Iron atom in the Crystal Structure of A Decolorizing Peroxidase (Dyp) That Catalyses the Biological Oxidation of Anthraquinone Derivatives (pdb code 2d3q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of A Decolorizing Peroxidase (Dyp) That Catalyses the Biological Oxidation of Anthraquinone Derivatives, PDB code: 2d3q:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of A Decolorizing Peroxidase (Dyp) That Catalyses the Biological Oxidation of Anthraquinone Derivatives


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Decolorizing Peroxidase (Dyp) That Catalyses the Biological Oxidation of Anthraquinone Derivatives within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe446 b:44.7 occ:1.00 FE A:HEM446 0.0 44.7 1.0 NC A:HEM446 2.1 39.4 1.0 ND A:HEM446 2.1 41.1 1.0 NA A:HEM446 2.1 44.9 1.0 NE2 A:HIS308 2.1 50.7 1.0 NB A:HEM446 2.2 44.0 1.0 CHB A:HEM446 2.7 45.9 1.0 C4A A:HEM446 3.0 47.9 1.0 C4C A:HEM446 3.1 40.5 1.0 CD2 A:HIS308 3.1 51.8 1.0 C1D A:HEM446 3.1 40.5 1.0 CE1 A:HIS308 3.1 51.2 1.0 CHD A:HEM446 3.1 38.4 1.0 C1B A:HEM446 3.1 45.3 1.0 C4D A:HEM446 3.1 43.6 1.0 CHA A:HEM446 3.2 44.8 1.0 C1C A:HEM446 3.2 41.0 1.0 C1A A:HEM446 3.2 46.7 1.0 CHC A:HEM446 3.3 43.3 1.0 C4B A:HEM446 3.3 45.2 1.0 ND1 A:HIS308 4.2 52.2 1.0 CG A:HIS308 4.2 53.5 1.0 NH1 A:ARG329 4.2 37.8 1.0 C2D A:HEM446 4.3 41.4 1.0 C3C A:HEM446 4.3 39.8 1.0 C3A A:HEM446 4.3 48.4 1.0 C2A A:HEM446 4.4 48.9 1.0 C2B A:HEM446 4.4 45.3 1.0 C3D A:HEM446 4.5 41.9 1.0 C2C A:HEM446 4.5 39.1 1.0 C3B A:HEM446 4.5 45.5 1.0 O A:HOH447 4.5 30.0 1.0 CD A:ARG329 4.9 37.4 1.0 CE1 A:PHE356 4.9 50.6 1.0

Iron binding site 2 out of 2 in the Crystal Structure of A Decolorizing Peroxidase (Dyp) That Catalyses the Biological Oxidation of Anthraquinone Derivatives


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Decolorizing Peroxidase (Dyp) That Catalyses the Biological Oxidation of Anthraquinone Derivatives within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe446 b:49.2 occ:1.00 FE B:HEM446 0.0 49.2 1.0 ND B:HEM446 2.1 51.8 1.0 NB B:HEM446 2.1 50.9 1.0 NE2 B:HIS308 2.1 50.2 1.0 NA B:HEM446 2.3 53.5 1.0 NC B:HEM446 2.3 49.8 1.0 CE1 B:HIS308 3.0 51.2 1.0 CHA B:HEM446 3.1 54.4 1.0 C4D B:HEM446 3.1 53.5 1.0 C1A B:HEM446 3.1 54.7 1.0 C4B B:HEM446 3.2 51.3 1.0 C1D B:HEM446 3.2 53.1 1.0 C1B B:HEM446 3.2 53.4 1.0 CD2 B:HIS308 3.2 52.3 1.0 C1C B:HEM446 3.2 50.6 1.0 CHD B:HEM446 3.2 51.5 1.0 CHB B:HEM446 3.2 55.1 1.0 C4C B:HEM446 3.3 49.9 1.0 C4A B:HEM446 3.3 54.9 1.0 CHC B:HEM446 3.3 51.3 1.0 ND1 B:HIS308 4.2 51.1 1.0 NH1 B:ARG329 4.3 49.2 1.0 CG B:HIS308 4.3 52.9 1.0 C3C B:HEM446 4.3 50.5 1.0 C2A B:HEM446 4.4 56.5 1.0 C3B B:HEM446 4.4 51.3 1.0 C2D B:HEM446 4.4 54.8 1.0 C3D B:HEM446 4.4 54.6 1.0 O B:HOH447 4.4 32.2 1.0 C3A B:HEM446 4.5 55.6 1.0 C2C B:HEM446 4.5 50.4 1.0 C2B B:HEM446 4.5 52.7 1.0 CD B:ARG329 4.7 51.8 1.0 CE1 B:PHE356 4.8 43.6 1.0 CZ B:ARG329 4.9 51.5 1.0

T.Yoshida, H.Tsuge, H.Konno, T.Hisabori, Y.Sugano. The Catalytic Mechanism of Dye-Decolorizing Peroxidase Dyp May Require the Swinging Movement of An Aspartic Acid Residue Febs J. V. 278 2387 2011.
ISSN: ISSN 1742-464X
PubMed: 21569205
DOI: 10.1111/J.1742-4658.2011.08161.X