Iron in PDB 7dlk: Crystal Structure of Veratryl Alcohol Bound Dye Decolorizing Peroxidase From Bacillus Subtilis

Protein crystallography data

The structure of Crystal Structure of Veratryl Alcohol Bound Dye Decolorizing Peroxidase From Bacillus Subtilis, PDB code: 7dlk 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) 45.68 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.988, 102.108, 105.47, 87.84, 76.45, 83.22
R / Rfree (%) 18.5 / 24.9

Other elements in 7dlk:

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

Chlorine (Cl) 8 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Veratryl Alcohol Bound Dye Decolorizing Peroxidase From Bacillus Subtilis (pdb code 7dlk). 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 Veratryl Alcohol Bound Dye Decolorizing Peroxidase From Bacillus Subtilis, PDB code: 7dlk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7dlk

Go back to Iron Binding Sites List in 7dlk
Iron binding site 1 out of 6 in the Crystal Structure of Veratryl Alcohol 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 Veratryl Alcohol Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:38.6
occ:0.50
FE A:HEM401 0.0 38.6 0.5
ND A:HEM401 1.9 34.9 1.0
NA A:HEM401 2.0 34.7 1.0
NC A:HEM401 2.1 32.0 1.0
NB A:HEM401 2.1 35.3 1.0
NE2 A:HIS273 2.1 46.5 1.0
O1 A:OXY402 2.9 57.5 1.0
C4D A:HEM401 2.9 32.6 1.0
C1D A:HEM401 2.9 32.7 1.0
C1A A:HEM401 3.0 33.2 1.0
C1B A:HEM401 3.0 32.3 1.0
C4C A:HEM401 3.0 34.9 1.0
CE1 A:HIS273 3.0 41.0 1.0
C4A A:HEM401 3.0 33.6 1.0
CD2 A:HIS273 3.1 42.7 1.0
C4B A:HEM401 3.1 34.9 1.0
C1C A:HEM401 3.2 35.8 1.0
CHB A:HEM401 3.4 32.6 1.0
CHA A:HEM401 3.4 33.0 1.0
CHD A:HEM401 3.4 31.9 1.0
CHC A:HEM401 3.6 35.5 1.0
O2 A:OXY402 3.9 66.0 1.0
ND1 A:HIS273 4.1 44.4 1.0
NH1 A:ARG286 4.1 31.0 1.0
CG A:HIS273 4.1 41.6 1.0
C3D A:HEM401 4.2 33.8 1.0
C2D A:HEM401 4.2 31.3 1.0
C2A A:HEM401 4.2 33.9 1.0
C3A A:HEM401 4.2 33.1 1.0
C3C A:HEM401 4.2 33.4 1.0
C2B A:HEM401 4.2 33.0 1.0
C3B A:HEM401 4.3 34.2 1.0
C2C A:HEM401 4.3 36.5 1.0
CD A:ARG286 4.5 29.7 1.0
CZ A:ARG286 4.9 33.4 1.0

Iron binding site 2 out of 6 in 7dlk

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Iron binding site 2 out of 6 in the Crystal Structure of Veratryl Alcohol 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 Veratryl Alcohol Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:40.4
occ:0.50
FE B:HEM401 0.0 40.4 0.5
ND B:HEM401 2.0 41.2 0.9
NA B:HEM401 2.0 35.1 1.0
NB B:HEM401 2.1 38.8 1.0
NC B:HEM401 2.1 35.3 1.0
NE2 B:HIS273 2.2 39.7 1.0
O2 B:OXY402 2.9 52.8 1.0
C1D B:HEM401 3.0 37.0 1.0
C4D B:HEM401 3.0 35.0 1.0
C1B B:HEM401 3.0 36.0 1.0
C1A B:HEM401 3.0 33.5 1.0
C4C B:HEM401 3.0 33.5 1.0
C4A B:HEM401 3.1 33.6 1.0
C4B B:HEM401 3.1 36.2 1.0
CE1 B:HIS273 3.1 37.1 1.0
C1C B:HEM401 3.1 38.8 1.0
CD2 B:HIS273 3.1 38.1 1.0
CHD B:HEM401 3.4 34.7 1.0
CHB B:HEM401 3.4 37.1 1.0
CHA B:HEM401 3.5 37.8 1.0
CHC B:HEM401 3.5 36.9 1.0
O1 B:OXY402 4.0 65.0 1.0
NH1 B:ARG286 4.0 39.3 1.0
ND1 B:HIS273 4.2 36.4 1.0
C2A B:HEM401 4.2 33.2 1.0
C2B B:HEM401 4.2 32.2 1.0
C3A B:HEM401 4.2 31.0 1.0
C2D B:HEM401 4.2 38.3 1.0
CG B:HIS273 4.3 39.9 1.0
C3B B:HEM401 4.3 35.2 1.0
C3D B:HEM401 4.3 36.3 1.0
C3C B:HEM401 4.3 33.0 1.0
C2C B:HEM401 4.3 36.9 1.0
CD B:ARG286 4.6 33.3 1.0
CZ B:ARG286 4.8 35.1 1.0

Iron binding site 3 out of 6 in 7dlk

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Iron binding site 3 out of 6 in the Crystal Structure of Veratryl Alcohol 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 Veratryl Alcohol Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:28.6
occ:0.50
FE C:HEM401 0.0 28.6 0.5
ND C:HEM401 1.9 33.7 1.0
NB C:HEM401 2.0 36.8 1.0
NA C:HEM401 2.0 30.6 1.0
NC C:HEM401 2.1 29.5 1.0
NE2 C:HIS273 2.1 36.1 1.0
O1 C:OXY402 2.7 44.4 1.0
C1D C:HEM401 3.0 33.4 1.0
C4D C:HEM401 3.0 31.9 1.0
C1B C:HEM401 3.0 34.2 1.0
C4B C:HEM401 3.0 33.3 1.0
CE1 C:HIS273 3.0 35.7 1.0
C4C C:HEM401 3.1 29.4 1.0
C1A C:HEM401 3.1 32.3 1.0
CD2 C:HIS273 3.1 36.4 1.0
C4A C:HEM401 3.1 29.7 1.0
C1C C:HEM401 3.1 30.5 1.0
CHB C:HEM401 3.4 32.3 1.0
CHD C:HEM401 3.4 29.1 1.0
CHA C:HEM401 3.5 33.7 1.0
CHC C:HEM401 3.5 30.4 1.0
O2 C:OXY402 3.9 49.9 1.0
NH1 C:ARG286 4.0 31.9 1.0
ND1 C:HIS273 4.1 37.5 1.0
CG C:HIS273 4.2 35.1 1.0
C2B C:HEM401 4.2 37.5 1.0
C2D C:HEM401 4.3 37.1 1.0
C3B C:HEM401 4.3 30.4 1.0
C3D C:HEM401 4.3 35.5 1.0
C3C C:HEM401 4.3 29.3 1.0
C3A C:HEM401 4.3 29.0 1.0
C2A C:HEM401 4.3 30.1 1.0
C2C C:HEM401 4.3 29.1 1.0
CD C:ARG286 4.7 29.9 1.0
CZ C:ARG286 4.9 33.8 1.0

Iron binding site 4 out of 6 in 7dlk

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Iron binding site 4 out of 6 in the Crystal Structure of Veratryl Alcohol 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 Veratryl Alcohol Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:31.4
occ:0.50
FE D:HEM401 0.0 31.4 0.5
ND D:HEM401 1.9 33.8 1.0
NA D:HEM401 2.0 33.5 1.0
NB D:HEM401 2.0 31.9 1.0
NC D:HEM401 2.1 32.2 1.0
NE2 D:HIS273 2.2 41.1 1.0
C1D D:HEM401 2.9 36.0 1.0
C4D D:HEM401 2.9 34.4 1.0
C1A D:HEM401 3.0 32.6 1.0
C4A D:HEM401 3.0 30.1 1.0
C4B D:HEM401 3.0 33.5 1.0
C1B D:HEM401 3.0 35.1 1.0
C4C D:HEM401 3.1 32.0 1.0
CE1 D:HIS273 3.1 39.7 1.0
C1C D:HEM401 3.1 33.9 1.0
CD2 D:HIS273 3.1 39.6 1.0
O2 D:OXY402 3.3 45.2 1.0
CHA D:HEM401 3.3 36.4 1.0
CHD D:HEM401 3.4 34.3 1.0
CHB D:HEM401 3.4 30.4 1.0
CHC D:HEM401 3.5 31.0 1.0
NH1 D:ARG286 4.0 30.2 1.0
ND1 D:HIS273 4.1 38.2 1.0
C2D D:HEM401 4.2 33.0 1.0
CG D:HIS273 4.2 46.0 1.0
C3D D:HEM401 4.2 30.2 1.0
O1 D:OXY402 4.2 58.6 1.0
C3A D:HEM401 4.2 32.7 1.0
C2A D:HEM401 4.2 34.4 1.0
C3B D:HEM401 4.3 31.8 1.0
C2B D:HEM401 4.3 30.5 1.0
C3C D:HEM401 4.3 31.7 1.0
C2C D:HEM401 4.3 30.7 1.0
CD D:ARG286 4.6 34.1 1.0
CZ D:ARG286 4.8 35.1 1.0

Iron binding site 5 out of 6 in 7dlk

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Iron binding site 5 out of 6 in the Crystal Structure of Veratryl Alcohol 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 Veratryl Alcohol Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:47.0
occ:0.50
FE E:HEM401 0.0 47.0 0.5
ND E:HEM401 1.9 45.1 1.0
NA E:HEM401 2.0 37.6 1.0
NB E:HEM401 2.1 41.5 1.0
NC E:HEM401 2.1 39.9 1.0
NE2 E:HIS273 2.3 41.0 0.9
C1D E:HEM401 3.0 40.4 1.0
C1A E:HEM401 3.0 41.9 1.0
C4D E:HEM401 3.0 38.3 1.0
O1 E:OXY402 3.0 55.5 1.0
C4A E:HEM401 3.0 43.4 1.0
C1B E:HEM401 3.0 39.4 1.0
C4C E:HEM401 3.0 40.5 1.0
C4B E:HEM401 3.1 42.0 1.0
C1C E:HEM401 3.1 44.8 1.0
CE1 E:HIS273 3.2 38.1 0.9
CD2 E:HIS273 3.2 42.4 0.9
CHA E:HEM401 3.4 41.3 1.0
CHD E:HEM401 3.4 43.4 1.0
CHB E:HEM401 3.5 40.1 1.0
CHC E:HEM401 3.5 44.3 1.0
NH1 E:ARG286 3.7 33.9 1.0
O2 E:OXY402 4.0 66.9 1.0
C2A E:HEM401 4.2 41.9 1.0
C3A E:HEM401 4.2 41.9 1.0
C2D E:HEM401 4.2 45.3 1.0
C3D E:HEM401 4.2 42.9 1.0
ND1 E:HIS273 4.3 40.7 0.9
C2B E:HEM401 4.3 38.8 1.0
C3C E:HEM401 4.3 45.6 1.0
CG E:HIS273 4.3 39.0 0.9
C2C E:HEM401 4.3 41.4 1.0
C3B E:HEM401 4.3 38.3 1.0
CD E:ARG286 4.6 36.6 1.0
CZ E:ARG286 4.7 38.1 1.0
NE E:ARG286 5.0 35.2 1.0

Iron binding site 6 out of 6 in 7dlk

Go back to Iron Binding Sites List in 7dlk
Iron binding site 6 out of 6 in the Crystal Structure of Veratryl Alcohol 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 Veratryl Alcohol Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:59.5
occ:0.90
FE F:HEM401 0.0 59.5 0.9
ND F:HEM401 1.9 53.2 1.0
NA F:HEM401 2.0 46.3 1.0
NC F:HEM401 2.0 40.3 1.0
NB F:HEM401 2.1 47.1 1.0
NE2 F:HIS273 2.3 59.8 1.0
C1D F:HEM401 2.9 43.0 1.0
C4D F:HEM401 2.9 38.1 1.0
C4C F:HEM401 3.0 44.9 1.0
C1A F:HEM401 3.0 44.7 1.0
C4A F:HEM401 3.1 43.0 1.0
C1B F:HEM401 3.1 44.8 1.0
C4B F:HEM401 3.1 44.6 1.0
C1C F:HEM401 3.1 46.3 1.0
CD2 F:HIS273 3.2 51.5 1.0
CE1 F:HIS273 3.3 53.9 1.0
CHD F:HEM401 3.4 41.0 1.0
O1 F:OXY402 3.4 58.6 1.0
CHA F:HEM401 3.4 45.3 1.0
CHB F:HEM401 3.5 43.3 1.0
CHC F:HEM401 3.6 43.5 1.0
O2 F:OXY402 3.7 62.0 1.0
C2D F:HEM401 4.2 40.1 1.0
C3C F:HEM401 4.2 35.8 1.0
C3D F:HEM401 4.2 46.5 1.0
NH1 F:ARG286 4.2 44.6 1.0
C3A F:HEM401 4.2 40.2 1.0
C2A F:HEM401 4.2 39.5 1.0
C2C F:HEM401 4.3 37.2 1.0
C2B F:HEM401 4.3 45.5 1.0
C3B F:HEM401 4.3 41.8 1.0
CG F:HIS273 4.4 60.2 1.0
ND1 F:HIS273 4.4 54.2 1.0
CD F:ARG286 4.4 51.9 1.0
CZ F:ARG286 4.8 44.5 1.0
NE F:ARG286 4.9 39.9 1.0

Reference:

P.Dhankhar, V.Dalal, V.Singh, A.K.Sharma, P.Kumar. Structure of Dye-Decolorizing Peroxidase From Bacillus Subtilis in Complex with Veratryl Alcohol. Int.J.Biol.Macromol. 2021.
ISSN: ISSN 0141-8130
PubMed: 34687768
DOI: 10.1016/J.IJBIOMAC.2021.10.100
Page generated: Fri Nov 5 13:58:38 2021

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