Iron in PDB 5de0: Dye-Decolorizing Protein From V. Cholerae

The structure of Dye-Decolorizing Protein From V. Cholerae, PDB code: 5de0 was solved by T.Uchida, M.Sasaki, Y.Tanaka, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.30 / 2.24
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	77.700, 77.700, 156.910, 90.00, 90.00, 120.00
R / Rfree (%)	23.6 / 24.8

The binding sites of Iron atom in the Dye-Decolorizing Protein From V. Cholerae (pdb code 5de0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dye-Decolorizing Protein From V. Cholerae, PDB code: 5de0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Dye-Decolorizing Protein From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dye-Decolorizing Protein From V. Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:31.2 occ:1.00 FE A:HEM401 0.0 31.2 1.0 NA A:HEM401 2.0 31.1 1.0 NC A:HEM401 2.1 36.7 1.0 ND A:HEM401 2.1 33.0 1.0 NB A:HEM401 2.1 32.9 1.0 NE2 A:HIS213 2.5 34.6 1.0 C1A A:HEM401 3.0 31.4 1.0 C4D A:HEM401 3.1 32.6 1.0 C4A A:HEM401 3.1 31.3 1.0 C1D A:HEM401 3.1 33.8 1.0 C4C A:HEM401 3.1 34.6 1.0 C1C A:HEM401 3.1 34.3 1.0 C1B A:HEM401 3.1 32.4 1.0 C4B A:HEM401 3.1 33.2 1.0 CD2 A:HIS213 3.1 34.3 1.0 CHA A:HEM401 3.4 31.6 1.0 CHD A:HEM401 3.4 34.4 1.0 CHB A:HEM401 3.5 31.7 1.0 CHC A:HEM401 3.5 33.9 1.0 CE1 A:HIS213 3.7 35.6 1.0 NH1 A:ARG230 4.0 30.8 1.0 C2A A:HEM401 4.3 30.9 1.0 C3A A:HEM401 4.3 30.7 1.0 C3C A:HEM401 4.3 35.1 1.0 C2C A:HEM401 4.3 35.2 1.0 C3D A:HEM401 4.3 33.4 1.0 C2D A:HEM401 4.3 34.1 1.0 C2B A:HEM401 4.3 32.3 1.0 C3B A:HEM401 4.3 32.8 1.0 CG A:HIS213 4.4 35.8 1.0 CE1 A:PHE246 4.6 33.6 1.0 ND1 A:HIS213 4.7 36.6 1.0 CD A:ARG230 4.8 33.0 1.0 OD1 A:ASP144 4.8 29.8 1.0 CZ A:ARG230 4.9 31.7 1.0 CG2 A:VAL217 5.0 38.3 1.0

Iron binding site 2 out of 4 in the Dye-Decolorizing Protein From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dye-Decolorizing Protein From V. Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:29.5 occ:1.00 FE B:HEM401 0.0 29.5 1.0 NC B:HEM401 2.0 25.4 1.0 NA B:HEM401 2.1 25.4 1.0 ND B:HEM401 2.1 25.5 1.0 NB B:HEM401 2.1 24.7 1.0 NE2 B:HIS213 2.6 29.9 1.0 O B:HOH546 2.8 24.2 1.0 C4C B:HEM401 3.0 24.8 1.0 C1D B:HEM401 3.1 24.2 1.0 C4A B:HEM401 3.1 23.7 1.0 C1A B:HEM401 3.1 24.8 1.0 C4D B:HEM401 3.1 24.1 1.0 C1B B:HEM401 3.1 23.3 1.0 C1C B:HEM401 3.1 23.7 1.0 C4B B:HEM401 3.1 22.6 1.0 CD2 B:HIS213 3.3 26.1 1.0 CHD B:HEM401 3.4 24.6 1.0 CHA B:HEM401 3.4 24.5 1.0 CHB B:HEM401 3.4 23.7 1.0 CHC B:HEM401 3.5 23.5 1.0 CE1 B:HIS213 3.7 27.4 1.0 NH1 B:ARG230 3.9 23.4 1.0 C3C B:HEM401 4.3 24.3 1.0 C2D B:HEM401 4.3 24.8 1.0 C2A B:HEM401 4.3 25.1 1.0 C3A B:HEM401 4.3 24.5 1.0 C3D B:HEM401 4.3 24.3 1.0 C2B B:HEM401 4.3 23.5 1.0 C2C B:HEM401 4.3 24.2 1.0 C3B B:HEM401 4.3 23.7 1.0 CG B:HIS213 4.5 29.0 1.0 CE1 B:PHE246 4.6 22.1 1.0 ND1 B:HIS213 4.7 27.2 1.0 CD B:ARG230 4.7 23.2 1.0 CZ B:ARG230 4.8 23.5 1.0 OD1 B:ASP144 4.8 24.3 1.0

Iron binding site 3 out of 4 in the Dye-Decolorizing Protein From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dye-Decolorizing Protein From V. Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:33.9 occ:1.00 FE C:HEM401 0.0 33.9 1.0 NA C:HEM401 2.0 28.5 1.0 NC C:HEM401 2.0 29.9 1.0 NB C:HEM401 2.1 29.4 1.0 ND C:HEM401 2.1 30.5 1.0 NE2 C:HIS213 2.5 36.4 1.0 O C:HOH547 3.0 26.8 1.0 C1A C:HEM401 3.0 29.4 1.0 C4C C:HEM401 3.0 29.4 1.0 C4A C:HEM401 3.0 27.9 1.0 C1B C:HEM401 3.1 27.8 1.0 C1C C:HEM401 3.1 29.2 1.0 C1D C:HEM401 3.1 29.1 1.0 C4D C:HEM401 3.1 28.8 1.0 C4B C:HEM401 3.1 27.7 1.0 CD2 C:HIS213 3.3 31.5 1.0 CHD C:HEM401 3.4 29.5 1.0 CHB C:HEM401 3.4 28.3 1.0 CHA C:HEM401 3.4 28.8 1.0 CHC C:HEM401 3.5 27.7 1.0 CE1 C:HIS213 3.6 31.5 1.0 NH1 C:ARG230 3.8 27.8 1.0 C2A C:HEM401 4.3 28.8 1.0 C3A C:HEM401 4.3 26.9 1.0 C3C C:HEM401 4.3 28.7 1.0 C2B C:HEM401 4.3 27.0 1.0 C2C C:HEM401 4.3 29.0 1.0 C3B C:HEM401 4.3 26.8 1.0 C2D C:HEM401 4.3 29.6 1.0 C3D C:HEM401 4.3 29.8 1.0 CG C:HIS213 4.6 32.8 1.0 CE1 C:PHE246 4.6 25.2 1.0 CD C:ARG230 4.6 32.1 1.0 CZ C:ARG230 4.7 28.0 1.0 ND1 C:HIS213 4.7 32.1 1.0 OD1 C:ASP144 4.8 29.2 1.0 NE C:ARG230 5.0 27.6 1.0

Iron binding site 4 out of 4 in the Dye-Decolorizing Protein From V. Cholerae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dye-Decolorizing Protein From V. Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:45.9 occ:1.00 FE D:HEM401 0.0 45.9 1.0 NA D:HEM401 2.0 44.3 1.0 NC D:HEM401 2.1 47.8 1.0 ND D:HEM401 2.1 47.2 1.0 NB D:HEM401 2.1 44.9 1.0 NE2 D:HIS213 2.7 48.9 1.0 C1A D:HEM401 3.1 44.5 1.0 C4A D:HEM401 3.1 44.4 1.0 C4C D:HEM401 3.1 48.1 1.0 C1D D:HEM401 3.1 48.2 1.0 C4D D:HEM401 3.1 46.7 1.0 C1C D:HEM401 3.1 47.1 1.0 C1B D:HEM401 3.1 43.8 1.0 C4B D:HEM401 3.1 45.6 1.0 CHD D:HEM401 3.4 48.2 1.0 CHA D:HEM401 3.4 45.0 1.0 CHB D:HEM401 3.4 44.2 1.0 CHC D:HEM401 3.5 46.4 1.0 CD2 D:HIS213 3.6 49.2 1.0 CE1 D:HIS213 3.7 49.5 1.0 NH1 D:ARG230 4.0 44.4 1.0 C2A D:HEM401 4.3 43.8 1.0 C3A D:HEM401 4.3 43.5 1.0 C3C D:HEM401 4.3 48.4 1.0 C2C D:HEM401 4.3 48.1 1.0 C2D D:HEM401 4.3 48.5 1.0 C3D D:HEM401 4.3 46.5 1.0 C2B D:HEM401 4.3 43.9 1.0 C3B D:HEM401 4.3 43.7 1.0 CE1 D:PHE246 4.5 46.7 1.0 CD D:ARG230 4.7 46.3 1.0 OD1 D:ASP144 4.8 42.9 1.0 CG D:HIS213 4.8 51.0 1.0 ND1 D:HIS213 4.8 51.3 1.0 CG1 D:VAL217 4.8 54.6 1.0 CD1 D:PHE246 5.0 46.0 1.0

T.Uchida, M.Sasaki, Y.Tanaka, K.Ishimori. A Dye-Decolorizing Peroxidase From Vibrio Cholerae. Biochemistry V. 54 6610 2015.
ISSN: ISSN 0006-2960
PubMed: 26431465
DOI: 10.1021/ACS.BIOCHEM.5B00952