Iron in PDB 7e5q: Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH

The structure of Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH, PDB code: 7e5q was solved by P.Dhankhar, V.Dalal, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.34 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.855, 117.342, 135.441, 90, 90, 90
R / Rfree (%)	18 / 23.3

The structure of Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH also contains other interesting chemical elements:

Sodium	(Na)	8 atoms
Chlorine	(Cl)	9 atoms

The binding sites of Iron atom in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH (pdb code 7e5q). 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 Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH, PDB code: 7e5q:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH


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 Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:36.7 occ:1.00 FE A:HEM401 0.0 36.7 1.0 NA A:HEM401 2.0 29.5 1.0 NB A:HEM401 2.1 28.2 1.0 NC A:HEM401 2.1 30.3 1.0 ND A:HEM401 2.1 31.6 1.0 NE2 A:HIS273 2.4 32.7 1.0 C4A A:HEM401 3.1 32.9 1.0 C1B A:HEM401 3.1 30.1 1.0 CD2 A:HIS273 3.1 28.6 1.0 C1A A:HEM401 3.1 32.7 1.0 C4C A:HEM401 3.1 29.5 1.0 C4D A:HEM401 3.1 30.1 1.0 C1D A:HEM401 3.1 30.2 1.0 C1C A:HEM401 3.1 29.8 1.0 C4B A:HEM401 3.1 34.0 1.0 O1 A:OXY402 3.2 39.2 1.0 CHB A:HEM401 3.4 28.0 1.0 CHA A:HEM401 3.4 28.3 1.0 CHD A:HEM401 3.4 28.2 1.0 CHC A:HEM401 3.5 35.3 1.0 CE1 A:HIS273 3.5 32.8 1.0 NH1 A:ARG286 4.1 25.6 1.0 C3A A:HEM401 4.3 25.7 1.0 C2A A:HEM401 4.3 30.8 1.0 C3C A:HEM401 4.3 36.2 1.0 C3D A:HEM401 4.3 33.0 1.0 C2D A:HEM401 4.3 35.6 1.0 C2B A:HEM401 4.3 26.8 1.0 CG A:HIS273 4.3 34.8 1.0 C2C A:HEM401 4.3 35.8 1.0 C3B A:HEM401 4.3 30.7 1.0 O2 A:OXY402 4.4 29.2 1.0 ND1 A:HIS273 4.5 34.6 1.0 CD A:ARG286 4.5 24.2 1.0 CZ A:ARG286 4.8 31.4 1.0 NE A:ARG286 4.9 32.8 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH


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 Dye Decolorizing Peroxidase From Bacillus Subtilis at Acidic pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:36.7 occ:1.00 FE B:HEM402 0.0 36.7 1.0 NA B:HEM402 2.0 32.8 1.0 NB B:HEM402 2.1 25.4 1.0 ND B:HEM402 2.1 30.6 1.0 NC B:HEM402 2.1 35.8 1.0 NE2 B:HIS273 2.4 31.9 1.0 C4A B:HEM402 3.0 33.0 1.0 CD2 B:HIS273 3.0 34.8 1.0 C1A B:HEM402 3.0 34.7 1.0 C4D B:HEM402 3.0 30.0 1.0 C1B B:HEM402 3.1 29.5 1.0 C4B B:HEM402 3.1 29.5 1.0 C1D B:HEM402 3.1 27.7 1.0 C1C B:HEM402 3.1 30.3 1.0 C4C B:HEM402 3.1 29.8 1.0 O2 B:OXY403 3.1 36.8 1.0 CHB B:HEM402 3.4 32.9 1.0 CHA B:HEM402 3.4 30.2 1.0 CHC B:HEM402 3.5 24.7 1.0 CHD B:HEM402 3.5 27.9 1.0 CE1 B:HIS273 3.6 39.1 1.0 NH1 B:ARG286 3.9 27.1 1.0 C3A B:HEM402 4.2 34.4 1.0 C2A B:HEM402 4.2 35.7 1.0 C3D B:HEM402 4.3 26.5 1.0 CG B:HIS273 4.3 33.4 1.0 C3B B:HEM402 4.3 24.8 1.0 C2B B:HEM402 4.3 24.7 1.0 C2D B:HEM402 4.3 33.7 1.0 C2C B:HEM402 4.3 30.9 1.0 C3C B:HEM402 4.3 29.7 1.0 O1 B:OXY403 4.4 30.9 1.0 ND1 B:HIS273 4.5 32.0 1.0 CD B:ARG286 4.6 30.4 1.0 CZ B:ARG286 4.7 32.7 1.0 CE1 B:PHE308 4.9 25.2 1.0 NE B:ARG286 5.0 29.8 1.0

P.Dhankhar, V.Dalal, A.K.Sharma, P.Kumar. Structural Insights at Acidic pH of Dye-Decolorizing Peroxidase From Bacillus Subtilis. Proteins 2022.
ISSN: ESSN 1097-0134
PubMed: 36345957
DOI: 10.1002/PROT.26444