Iron in PDB 6kmm: Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis

The structure of Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis, PDB code: 6kmm was solved by P.Dhankhar, V.Dalal, J.K.Mahto, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.91 / 1.93
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	79.837, 101.905, 105.405, 88.00, 76.43, 83.28
R / Rfree (%)	16.1 / 20.2

The structure of Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Iron atom in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis (pdb code 6kmm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis, PDB code: 6kmm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis


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 Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:34.4 occ:0.90 FE A:HEM401 0.0 34.4 0.9 ND A:HEM401 2.0 30.7 1.0 NA A:HEM401 2.0 30.6 1.0 NB A:HEM401 2.1 30.6 1.0 NC A:HEM401 2.1 30.8 1.0 NE2 A:HIS273 2.2 32.3 1.0 O1 A:OXY402 2.7 45.4 1.0 C1D A:HEM401 3.0 31.3 1.0 C1B A:HEM401 3.0 29.9 1.0 C4D A:HEM401 3.0 30.0 1.0 C4C A:HEM401 3.0 30.0 1.0 C4A A:HEM401 3.0 30.9 1.0 CD2 A:HIS273 3.1 32.0 1.0 C1A A:HEM401 3.1 30.8 1.0 C4B A:HEM401 3.1 30.9 1.0 C1C A:HEM401 3.1 30.9 1.0 CE1 A:HIS273 3.2 33.8 1.0 CHB A:HEM401 3.4 29.5 1.0 CHD A:HEM401 3.4 30.6 1.0 CHC A:HEM401 3.5 31.5 1.0 CHA A:HEM401 3.5 30.1 1.0 O2 A:OXY402 4.0 47.6 1.0 NH1 A:ARG286 4.0 29.2 1.0 C3C A:HEM401 4.2 31.5 1.0 CG A:HIS273 4.2 32.3 1.0 C3A A:HEM401 4.2 29.4 1.0 ND1 A:HIS273 4.3 32.8 1.0 C2B A:HEM401 4.3 30.3 1.0 C2D A:HEM401 4.3 29.0 1.0 C2A A:HEM401 4.3 30.5 1.0 C3D A:HEM401 4.3 29.0 1.0 C2C A:HEM401 4.3 31.7 1.0 C3B A:HEM401 4.3 29.9 1.0 CD A:ARG286 4.6 32.2 1.0 CZ A:ARG286 4.9 30.7 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis


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 Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:31.4 occ:0.70 FE B:HEM401 0.0 31.4 0.7 ND B:HEM401 1.9 31.7 1.0 NA B:HEM401 2.0 31.4 1.0 NC B:HEM401 2.0 31.8 1.0 NB B:HEM401 2.1 32.8 1.0 NE2 B:HIS273 2.2 34.3 1.0 O2 B:OXY402 2.9 46.0 1.0 C1D B:HEM401 2.9 32.9 1.0 C4B B:HEM401 3.0 31.5 1.0 C4D B:HEM401 3.0 30.8 1.0 C1C B:HEM401 3.0 31.5 1.0 C4C B:HEM401 3.0 32.5 1.0 C1A B:HEM401 3.1 31.3 1.0 C1B B:HEM401 3.1 32.1 1.0 CD2 B:HIS273 3.1 31.6 1.0 C4A B:HEM401 3.1 32.7 1.0 CE1 B:HIS273 3.2 35.4 1.0 CHC B:HEM401 3.4 32.4 1.0 CHD B:HEM401 3.4 34.0 1.0 CHA B:HEM401 3.5 32.7 1.0 CHB B:HEM401 3.5 32.1 1.0 O1 B:OXY402 4.1 56.8 1.0 NH1 B:ARG286 4.1 28.7 1.0 C2C B:HEM401 4.2 33.0 1.0 C2D B:HEM401 4.2 32.6 1.0 C3B B:HEM401 4.2 31.6 1.0 C3C B:HEM401 4.2 31.9 1.0 C3D B:HEM401 4.2 32.5 1.0 C2B B:HEM401 4.3 31.3 1.0 CG B:HIS273 4.3 33.3 1.0 C2A B:HEM401 4.3 32.4 1.0 ND1 B:HIS273 4.3 34.1 1.0 C3A B:HEM401 4.3 30.2 1.0 CD B:ARG286 4.7 31.6 1.0 CZ B:ARG286 4.9 32.0 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis


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 Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:37.8 occ:1.00 FE C:HEM401 0.0 37.8 1.0 ND C:HEM401 1.9 34.2 1.0 NA C:HEM401 2.0 33.1 1.0 NB C:HEM401 2.1 33.4 1.0 NE2 C:HIS273 2.1 36.5 1.0 NC C:HEM401 2.1 33.1 1.0 O1 C:OXY402 2.7 54.5 1.0 C1D C:HEM401 2.9 34.4 1.0 C4D C:HEM401 3.0 34.3 1.0 C4C C:HEM401 3.0 33.2 1.0 CE1 C:HIS273 3.0 37.2 1.0 C4B C:HEM401 3.0 33.6 1.0 C1A C:HEM401 3.0 32.8 1.0 C1B C:HEM401 3.0 32.5 1.0 C4A C:HEM401 3.1 31.6 1.0 CD2 C:HIS273 3.1 37.6 1.0 C1C C:HEM401 3.1 33.0 1.0 CHD C:HEM401 3.4 33.7 1.0 CHA C:HEM401 3.4 32.4 1.0 CHB C:HEM401 3.4 31.8 1.0 CHC C:HEM401 3.5 32.9 1.0 O2 C:OXY402 3.8 48.4 1.0 NH1 C:ARG286 4.0 31.1 1.0 ND1 C:HIS273 4.1 37.1 1.0 CG C:HIS273 4.2 36.9 1.0 C3D C:HEM401 4.2 33.3 1.0 C2D C:HEM401 4.2 34.4 1.0 C3A C:HEM401 4.3 33.4 1.0 C3B C:HEM401 4.3 32.2 1.0 C2B C:HEM401 4.3 31.1 1.0 C3C C:HEM401 4.3 34.3 1.0 C2A C:HEM401 4.3 34.4 1.0 C2C C:HEM401 4.3 32.4 1.0 CD C:ARG286 4.6 32.1 1.0 CZ C:ARG286 4.8 34.6 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis


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 Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:31.1 occ:0.90 FE D:HEM401 0.0 31.1 0.9 ND D:HEM401 2.0 30.5 1.0 NB D:HEM401 2.0 30.2 1.0 NA D:HEM401 2.0 30.4 1.0 NC D:HEM401 2.1 28.5 1.0 NE2 D:HIS273 2.1 34.2 1.0 O1 D:OXY402 2.6 46.1 1.0 C4B D:HEM401 3.0 30.2 1.0 C1B D:HEM401 3.0 30.2 1.0 C1D D:HEM401 3.0 28.3 1.0 C4C D:HEM401 3.0 28.3 1.0 CE1 D:HIS273 3.0 32.2 1.0 CD2 D:HIS273 3.0 32.3 1.0 C4A D:HEM401 3.0 27.5 1.0 C4D D:HEM401 3.1 29.0 1.0 C1A D:HEM401 3.1 28.1 1.0 C1C D:HEM401 3.1 29.5 1.0 CHC D:HEM401 3.4 29.4 1.0 CHD D:HEM401 3.4 28.4 1.0 CHB D:HEM401 3.4 28.7 1.0 CHA D:HEM401 3.5 28.6 1.0 O2 D:OXY402 3.8 48.7 1.0 NH1 D:ARG286 4.1 31.7 1.0 ND1 D:HIS273 4.1 30.9 1.0 CG D:HIS273 4.2 32.6 1.0 C3B D:HEM401 4.2 31.0 1.0 C2B D:HEM401 4.2 29.7 1.0 C3A D:HEM401 4.2 27.2 1.0 C3C D:HEM401 4.2 28.3 1.0 C2A D:HEM401 4.3 28.6 1.0 C2D D:HEM401 4.3 30.5 1.0 C2C D:HEM401 4.3 29.6 1.0 C3D D:HEM401 4.3 29.4 1.0 CD D:ARG286 4.6 29.9 1.0 CZ D:ARG286 4.9 32.4 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:40.9 occ:0.90 FE E:HEM401 0.0 40.9 0.9 ND E:HEM401 1.9 39.1 1.0 NA E:HEM401 2.0 36.3 1.0 NB E:HEM401 2.1 38.1 1.0 NC E:HEM401 2.1 37.9 1.0 NE2 E:HIS273 2.2 37.1 1.0 O2 E:OXY402 2.6 59.5 1.0 C1D E:HEM401 3.0 38.5 1.0 C4D E:HEM401 3.0 38.5 1.0 C4A E:HEM401 3.0 37.0 1.0 C1A E:HEM401 3.0 37.8 1.0 C4B E:HEM401 3.1 37.0 1.0 C1B E:HEM401 3.1 36.8 1.0 C4C E:HEM401 3.1 38.4 1.0 CD2 E:HIS273 3.1 36.6 1.0 C1C E:HEM401 3.1 38.0 1.0 CE1 E:HIS273 3.2 38.1 1.0 CHB E:HEM401 3.4 36.7 1.0 CHD E:HEM401 3.4 39.0 1.0 CHA E:HEM401 3.5 37.5 1.0 CHC E:HEM401 3.5 35.3 1.0 O1 E:OXY402 3.8 60.1 1.0 NH1 E:ARG286 4.0 38.0 1.0 C3A E:HEM401 4.2 37.5 1.0 C2D E:HEM401 4.2 37.5 1.0 CG E:HIS273 4.2 37.5 1.0 C2A E:HEM401 4.2 37.6 1.0 C3D E:HEM401 4.3 37.7 1.0 C2B E:HEM401 4.3 36.9 1.0 C3B E:HEM401 4.3 35.9 1.0 ND1 E:HIS273 4.3 37.2 1.0 C3C E:HEM401 4.3 40.7 1.0 C2C E:HEM401 4.4 39.5 1.0 CD E:ARG286 4.6 37.9 1.0 CZ E:ARG286 4.8 37.8 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe401 b:47.9 occ:1.00 FE F:HEM401 0.0 47.9 1.0 ND F:HEM401 1.9 44.9 1.0 NA F:HEM401 2.1 44.5 1.0 NB F:HEM401 2.1 43.3 1.0 NC F:HEM401 2.1 42.8 1.0 NE2 F:HIS273 2.2 45.1 1.0 O2 F:OXY402 2.9 55.6 1.0 C1D F:HEM401 2.9 45.2 1.0 C4D F:HEM401 3.0 45.1 1.0 C4C F:HEM401 3.0 45.0 1.0 C1B F:HEM401 3.0 42.7 1.0 C4B F:HEM401 3.0 42.8 1.0 C1A F:HEM401 3.1 44.8 1.0 C4A F:HEM401 3.1 44.1 1.0 CD2 F:HIS273 3.1 45.5 1.0 C1C F:HEM401 3.1 43.0 1.0 CE1 F:HIS273 3.2 45.4 1.0 CHD F:HEM401 3.4 44.7 1.0 CHB F:HEM401 3.4 41.9 1.0 CHA F:HEM401 3.5 45.1 1.0 CHC F:HEM401 3.5 41.3 1.0 NH1 F:ARG286 4.1 46.5 1.0 O1 F:OXY402 4.1 54.1 1.0 C2D F:HEM401 4.2 46.5 1.0 C3D F:HEM401 4.2 46.2 1.0 C3C F:HEM401 4.3 43.5 1.0 CG F:HIS273 4.3 45.6 1.0 C2B F:HEM401 4.3 42.4 1.0 C2A F:HEM401 4.3 44.7 1.0 C3B F:HEM401 4.3 42.1 1.0 ND1 F:HIS273 4.3 45.1 1.0 C3A F:HEM401 4.3 43.8 1.0 C2C F:HEM401 4.3 42.9 1.0 CD F:ARG286 4.6 45.5 1.0 CZ F:ARG286 4.9 46.2 1.0

P.Dhankhar, V.Dalal, J.K.Mahto, B.R.Gurjar, S.Tomar, A.K.Sharma, P.Kumar. Characterization of Dye-Decolorizing Peroxidase From Bacillus Subtilis. Arch.Biochem.Biophys. V. 693 08590 2020.
ISSN: ESSN 1096-0384
PubMed: 32971035
DOI: 10.1016/J.ABB.2020.108590