Iron in PDB 5gt2: Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157

The structure of Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157, PDB code: 5gt2 was solved by Y.L.Ma, Z.G.Yuan, S.Liu, J.X.Wang, L.C.Gu, X.H.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.69 / 2.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.574, 101.597, 114.300, 90.00, 111.51, 90.00
R / Rfree (%)	22 / 24.8

The binding sites of Iron atom in the Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157 (pdb code 5gt2). 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 and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157, PDB code: 5gt2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.7 occ:1.00 FE A:HEM401 0.0 21.7 1.0 NA A:HEM401 2.0 22.7 1.0 ND A:HEM401 2.0 21.0 1.0 NB A:HEM401 2.0 22.0 1.0 NC A:HEM401 2.0 22.4 1.0 NE2 A:HIS216 2.4 19.9 1.0 O A:HOH667 2.9 34.2 1.0 C1D A:HEM401 3.0 20.4 1.0 C4A A:HEM401 3.0 21.4 1.0 C4C A:HEM401 3.0 21.2 1.0 C1B A:HEM401 3.1 20.5 1.0 C1A A:HEM401 3.1 22.1 1.0 C4B A:HEM401 3.1 20.7 1.0 C4D A:HEM401 3.1 20.7 1.0 C1C A:HEM401 3.1 21.4 1.0 CE1 A:HIS216 3.2 19.6 1.0 CD2 A:HIS216 3.4 19.9 1.0 CHD A:HEM401 3.4 19.5 1.0 CHB A:HEM401 3.4 20.4 1.0 CHA A:HEM401 3.4 22.0 1.0 CHC A:HEM401 3.4 20.3 1.0 NH1 A:ARG233 4.1 18.0 1.0 C3A A:HEM401 4.3 21.5 1.0 C2A A:HEM401 4.3 22.6 1.0 C2D A:HEM401 4.3 20.3 1.0 C3C A:HEM401 4.3 21.6 1.0 C2B A:HEM401 4.3 21.7 1.0 C3B A:HEM401 4.3 21.5 1.0 C3D A:HEM401 4.3 21.5 1.0 C2C A:HEM401 4.3 21.3 1.0 ND1 A:HIS216 4.4 20.6 1.0 CG A:HIS216 4.5 21.1 1.0 CD A:ARG233 4.6 18.9 1.0 OD1 A:ASP144 4.6 23.1 1.0 CE1 A:PHE249 4.7 18.1 1.0 CZ A:ARG233 4.9 20.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:20.8 occ:1.00 FE B:HEM401 0.0 20.8 1.0 NC B:HEM401 2.0 21.3 1.0 NB B:HEM401 2.0 20.9 1.0 NA B:HEM401 2.1 21.1 1.0 ND B:HEM401 2.1 20.7 1.0 NE2 B:HIS216 2.3 22.1 1.0 O B:HOH647 2.8 29.5 1.0 C4C B:HEM401 3.0 22.6 1.0 C4B B:HEM401 3.0 23.1 1.0 C1C B:HEM401 3.0 22.1 1.0 C1D B:HEM401 3.0 22.6 1.0 C4A B:HEM401 3.1 21.6 1.0 C1B B:HEM401 3.1 21.6 1.0 C1A B:HEM401 3.1 22.6 1.0 C4D B:HEM401 3.1 22.9 1.0 CD2 B:HIS216 3.3 21.8 1.0 CE1 B:HIS216 3.3 21.4 1.0 CHC B:HEM401 3.4 22.1 1.0 CHD B:HEM401 3.4 22.2 1.0 CHB B:HEM401 3.4 21.4 1.0 CHA B:HEM401 3.5 23.2 1.0 NH1 B:ARG233 4.0 19.6 1.0 C3C B:HEM401 4.3 21.8 1.0 C2C B:HEM401 4.3 21.5 1.0 C3B B:HEM401 4.3 23.1 1.0 C2D B:HEM401 4.3 20.2 1.0 C3A B:HEM401 4.3 21.9 1.0 C2B B:HEM401 4.3 22.3 1.0 C2A B:HEM401 4.3 23.4 1.0 C3D B:HEM401 4.3 22.3 1.0 ND1 B:HIS216 4.4 22.7 1.0 CG B:HIS216 4.4 22.9 1.0 CD B:ARG233 4.5 24.4 1.0 CE1 B:PHE249 4.6 21.3 1.0 OD1 B:ASP144 4.6 23.9 1.0 CZ B:ARG233 4.8 22.8 1.0 NE B:ARG233 5.0 24.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:30.1 occ:1.00 FE C:HEM401 0.0 30.1 1.0 NA C:HEM401 2.0 31.2 1.0 NC C:HEM401 2.0 30.6 1.0 ND C:HEM401 2.0 31.4 1.0 NB C:HEM401 2.1 29.2 1.0 NE2 C:HIS216 2.4 30.9 1.0 C4C C:HEM401 3.0 32.7 1.0 C1D C:HEM401 3.1 33.3 1.0 C1A C:HEM401 3.1 34.2 1.0 C4A C:HEM401 3.1 30.7 1.0 C1C C:HEM401 3.1 29.8 1.0 C4D C:HEM401 3.1 33.0 1.0 C1B C:HEM401 3.1 29.1 1.0 C4B C:HEM401 3.1 29.5 1.0 O C:HOH643 3.2 29.4 1.0 CE1 C:HIS216 3.3 32.2 1.0 CD2 C:HIS216 3.3 31.9 1.0 CHD C:HEM401 3.4 33.5 1.0 CHA C:HEM401 3.4 33.9 1.0 CHB C:HEM401 3.4 28.9 1.0 CHC C:HEM401 3.4 28.7 1.0 NH1 C:ARG233 4.0 29.6 1.0 C3C C:HEM401 4.3 32.5 1.0 C3A C:HEM401 4.3 32.2 1.0 C2A C:HEM401 4.3 33.9 1.0 C2D C:HEM401 4.3 33.0 1.0 C2C C:HEM401 4.3 30.0 1.0 C3D C:HEM401 4.3 33.1 1.0 C2B C:HEM401 4.3 29.0 1.0 C3B C:HEM401 4.3 29.2 1.0 ND1 C:HIS216 4.4 33.5 1.0 CG C:HIS216 4.5 33.7 1.0 OD1 C:ASP144 4.6 36.6 1.0 CE2 C:PHE249 4.6 22.6 1.0 CD C:ARG233 4.6 30.7 1.0 CZ C:ARG233 4.8 32.1 1.0

Iron binding site 4 out of 4 in the Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:38.8 occ:1.00 FE D:HEM401 0.0 38.8 1.0 NA D:HEM401 2.0 38.7 1.0 NC D:HEM401 2.0 37.5 1.0 NB D:HEM401 2.1 37.7 1.0 ND D:HEM401 2.1 41.6 1.0 NE2 D:HIS216 2.3 51.9 1.0 O D:HOH579 2.8 29.9 1.0 C4A D:HEM401 3.0 37.0 1.0 C1B D:HEM401 3.1 36.6 1.0 C4C D:HEM401 3.1 38.7 1.0 C1A D:HEM401 3.1 40.3 1.0 C1C D:HEM401 3.1 35.6 1.0 C4B D:HEM401 3.1 35.5 1.0 C1D D:HEM401 3.1 42.4 1.0 C4D D:HEM401 3.1 42.1 1.0 CE1 D:HIS216 3.3 53.0 1.0 CD2 D:HIS216 3.3 52.7 1.0 CHB D:HEM401 3.4 36.4 1.0 CHD D:HEM401 3.4 40.5 1.0 CHC D:HEM401 3.4 35.4 1.0 CHA D:HEM401 3.5 40.9 1.0 NH1 D:ARG233 4.1 31.8 1.0 C3A D:HEM401 4.3 37.6 1.0 C2A D:HEM401 4.3 40.4 1.0 C2B D:HEM401 4.3 35.5 1.0 C3C D:HEM401 4.3 37.3 1.0 C2C D:HEM401 4.3 35.2 1.0 C3B D:HEM401 4.3 35.1 1.0 C2D D:HEM401 4.3 44.4 1.0 C3D D:HEM401 4.3 45.2 1.0 ND1 D:HIS216 4.4 54.8 1.0 CG D:HIS216 4.5 54.8 1.0 CE2 D:PHE249 4.5 26.4 1.0 CD D:ARG233 4.7 33.0 1.0 OD1 D:ASP144 4.7 45.7 1.0 CZ D:ARG233 4.9 33.2 1.0 CD2 D:PHE249 4.9 25.8 1.0

X.Liu, Z.Yuan, J.Wang, Y.Cui, S.Liu, Y.Ma, L.Gu, S.Xu. Crystal Structure and Biochemical Features of Dye-Decolorizing Peroxidase Yfex From Escherichia Coli O157 Asp(143) and Arg(232) Play Divergent Roles Toward Different Substrates Biochem. Biophys. Res. V. 484 40 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28109884
DOI: 10.1016/J.BBRC.2017.01.081