Iron in PDB 4w7j: Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae

All present enzymatic activity of Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae:
1.11.1.19;

The structure of Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae, PDB code: 4w7j was solved by F.J.Medrano, A.Romero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.36 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	154.220, 100.500, 128.630, 90.00, 123.69, 90.00
R / Rfree (%)	19.4 / 24.2

The binding sites of Iron atom in the Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae (pdb code 4w7j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae, PDB code: 4w7j:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae


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) From Auricularia Auricula-Judae within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.8 occ:1.00 FE A:HEM501 0.0 19.8 1.0 NA A:HEM501 2.0 18.0 1.0 NC A:HEM501 2.0 16.8 1.0 NB A:HEM501 2.1 18.2 1.0 ND A:HEM501 2.1 19.1 1.0 NE2 A:HIS304 2.3 19.9 1.0 O A:HOH658 2.6 27.8 1.0 C4A A:HEM501 3.0 20.1 1.0 C1B A:HEM501 3.0 20.9 1.0 C4C A:HEM501 3.0 19.7 1.0 C1A A:HEM501 3.0 18.5 1.0 C1D A:HEM501 3.1 20.0 1.0 C4D A:HEM501 3.1 19.9 1.0 C1C A:HEM501 3.1 15.8 1.0 C4B A:HEM501 3.1 19.3 1.0 CD2 A:HIS304 3.1 18.7 1.0 CE1 A:HIS304 3.3 20.1 1.0 CHB A:HEM501 3.4 19.2 1.0 CHD A:HEM501 3.4 19.4 1.0 CHA A:HEM501 3.4 18.1 1.0 CHC A:HEM501 3.5 17.0 1.0 NH1 A:ARG332 4.2 21.3 1.0 C3A A:HEM501 4.2 19.9 1.0 C2A A:HEM501 4.3 17.8 1.0 C3C A:HEM501 4.3 19.9 1.0 C2B A:HEM501 4.3 20.9 1.0 C2C A:HEM501 4.3 17.7 1.0 C3D A:HEM501 4.3 17.3 1.0 C2D A:HEM501 4.3 21.5 1.0 C3B A:HEM501 4.3 17.9 1.0 CG A:HIS304 4.3 23.4 1.0 ND1 A:HIS304 4.4 21.0 1.0 CD A:ARG332 4.7 18.4 1.0 CZ A:ARG332 5.0 21.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae


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) From Auricularia Auricula-Judae within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:20.2 occ:1.00 FE B:HEM501 0.0 20.2 1.0 NB B:HEM501 2.0 19.6 1.0 NC B:HEM501 2.0 20.8 1.0 NA B:HEM501 2.1 17.2 1.0 ND B:HEM501 2.1 17.6 1.0 NE2 B:HIS304 2.3 22.3 1.0 O B:HOH743 2.5 28.9 1.0 C4B B:HEM501 3.0 21.7 1.0 C1B B:HEM501 3.0 18.5 1.0 C1C B:HEM501 3.0 20.8 1.0 C4C B:HEM501 3.1 21.4 1.0 C4A B:HEM501 3.1 18.9 1.0 C1A B:HEM501 3.1 18.5 1.0 C4D B:HEM501 3.1 17.5 1.0 CD2 B:HIS304 3.1 19.6 1.0 C1D B:HEM501 3.1 20.1 1.0 CE1 B:HIS304 3.4 21.7 1.0 CHC B:HEM501 3.4 21.0 1.0 CHB B:HEM501 3.4 21.9 1.0 CHA B:HEM501 3.4 20.1 1.0 CHD B:HEM501 3.5 18.2 1.0 NH1 B:ARG332 4.2 18.7 1.0 C3B B:HEM501 4.3 17.9 1.0 C2B B:HEM501 4.3 19.9 1.0 C2C B:HEM501 4.3 22.7 1.0 C3C B:HEM501 4.3 21.8 1.0 C3A B:HEM501 4.3 21.0 1.0 CG B:HIS304 4.3 19.0 1.0 C2A B:HEM501 4.3 20.6 1.0 C3D B:HEM501 4.3 19.6 1.0 C2D B:HEM501 4.3 18.9 1.0 ND1 B:HIS304 4.4 19.0 1.0 CD B:ARG332 4.8 20.2 1.0 CZ B:ARG332 5.0 21.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:20.3 occ:1.00 FE C:HEM501 0.0 20.3 1.0 NB C:HEM501 2.0 19.5 1.0 NA C:HEM501 2.0 18.8 1.0 NC C:HEM501 2.1 18.9 1.0 ND C:HEM501 2.1 18.5 1.0 NE2 C:HIS304 2.3 17.8 1.0 O C:HOH753 2.8 27.5 1.0 C4A C:HEM501 3.1 19.0 1.0 C1B C:HEM501 3.1 23.2 1.0 C1C C:HEM501 3.1 17.6 1.0 C1D C:HEM501 3.1 17.3 1.0 C4C C:HEM501 3.1 18.6 1.0 C1A C:HEM501 3.1 18.0 1.0 C4D C:HEM501 3.1 18.5 1.0 C4B C:HEM501 3.1 19.7 1.0 CD2 C:HIS304 3.1 18.8 1.0 CE1 C:HIS304 3.3 17.8 1.0 CHB C:HEM501 3.4 21.1 1.0 CHA C:HEM501 3.4 17.4 1.0 CHD C:HEM501 3.4 17.1 1.0 CHC C:HEM501 3.4 18.8 1.0 NH1 C:ARG332 4.2 18.2 1.0 C3A C:HEM501 4.3 19.8 1.0 C2C C:HEM501 4.3 16.9 1.0 C3C C:HEM501 4.3 15.8 1.0 C2B C:HEM501 4.3 22.4 1.0 C2A C:HEM501 4.3 20.4 1.0 CG C:HIS304 4.3 19.0 1.0 C3B C:HEM501 4.3 17.9 1.0 C2D C:HEM501 4.3 16.1 1.0 C3D C:HEM501 4.3 15.5 1.0 ND1 C:HIS304 4.4 16.0 1.0 CD C:ARG332 4.7 20.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Decolorizing Peroxidase (Dyp) From Auricularia Auricula-Judae within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:20.3 occ:1.00 FE D:HEM501 0.0 20.3 1.0 NB D:HEM501 2.0 18.7 1.0 NC D:HEM501 2.0 19.4 1.0 NA D:HEM501 2.1 16.5 1.0 ND D:HEM501 2.1 19.5 1.0 NE2 D:HIS304 2.3 21.2 1.0 O D:HOH697 2.4 24.6 1.0 C1B D:HEM501 3.0 15.9 1.0 C4C D:HEM501 3.0 17.9 1.0 C4B D:HEM501 3.0 19.0 1.0 C1C D:HEM501 3.0 18.2 1.0 C4A D:HEM501 3.1 20.5 1.0 C1D D:HEM501 3.1 17.4 1.0 C1A D:HEM501 3.1 16.9 1.0 CD2 D:HIS304 3.1 18.2 1.0 C4D D:HEM501 3.1 20.2 1.0 CE1 D:HIS304 3.3 20.8 1.0 CHB D:HEM501 3.4 18.7 1.0 CHD D:HEM501 3.4 19.7 1.0 CHC D:HEM501 3.4 16.7 1.0 CHA D:HEM501 3.5 18.9 1.0 NH1 D:ARG332 4.2 18.3 1.0 C2B D:HEM501 4.2 18.3 1.0 C3C D:HEM501 4.3 19.4 1.0 C2C D:HEM501 4.3 17.7 1.0 C3B D:HEM501 4.3 17.3 1.0 C3A D:HEM501 4.3 20.0 1.0 C2A D:HEM501 4.3 17.7 1.0 CG D:HIS304 4.3 20.9 1.0 C2D D:HEM501 4.3 17.1 1.0 C3D D:HEM501 4.4 16.5 1.0 ND1 D:HIS304 4.4 21.0 1.0 CD D:ARG332 4.8 19.7 1.0

D.Linde, R.Pogni, M.Canellas, F.Lucas, V.Guallar, M.C.Baratto, A.Sinicropi, V.Saez-Jimenez, C.Coscolin, A.Romero, F.J.Medrano, F.J.Ruiz-Duenas, A.T.Martinez. Catalytic Surface Radical in Dye-Decolorizing Peroxidase: A Computational, Spectroscopic and Site-Directed Mutagenesis Study. Biochem.J. V. 466 253 2015.
ISSN: ESSN 1470-8728
PubMed: 25495127
DOI: 10.1042/BJ20141211