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Iron in PDB 6qzo: Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis

Protein crystallography data

The structure of Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis, PDB code: 6qzo was solved by H.J.Rozeboom, M.W.Fraaije, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.87 / 2.40
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 173.989, 173.989, 283.003, 90.00, 90.00, 120.00
R / Rfree (%) 24.2 / 26.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis (pdb code 6qzo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis, PDB code: 6qzo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6qzo

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Iron binding site 1 out of 8 in the Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis


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 Dyp-Type Peroxidase From Cellulomonas Bogoriensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:20.9
occ:1.00
FE A:HEM401 0.0 20.9 1.0
ND A:HEM401 1.9 21.1 1.0
NA A:HEM401 2.0 21.2 1.0
NE2 A:HIS292 2.1 19.4 1.0
NC A:HEM401 2.1 20.3 1.0
NB A:HEM401 2.1 20.7 1.0
C4D A:HEM401 2.9 21.5 1.0
C1D A:HEM401 2.9 20.5 1.0
C1A A:HEM401 3.0 21.5 1.0
C4A A:HEM401 3.0 21.7 1.0
CD2 A:HIS292 3.1 20.1 1.0
C4B A:HEM401 3.1 20.6 1.0
C1B A:HEM401 3.1 20.6 1.0
C4C A:HEM401 3.1 20.4 1.0
C1C A:HEM401 3.1 20.8 1.0
CE1 A:HIS292 3.1 19.8 1.0
CHA A:HEM401 3.3 21.5 1.0
CHD A:HEM401 3.4 21.0 1.0
CHB A:HEM401 3.5 20.9 1.0
CHC A:HEM401 3.5 21.2 1.0
C3D A:HEM401 4.2 22.1 1.0
C2D A:HEM401 4.2 21.3 1.0
NH1 A:ARG307 4.2 15.2 1.0
C2A A:HEM401 4.2 22.1 1.0
C3A A:HEM401 4.2 22.4 1.0
CG A:HIS292 4.2 20.3 1.0
ND1 A:HIS292 4.2 19.9 1.0
C2C A:HEM401 4.3 20.5 1.0
C3C A:HEM401 4.3 21.0 1.0
C2B A:HEM401 4.3 21.6 1.0
C3B A:HEM401 4.3 20.7 1.0
OE1 A:GLU201 4.4 35.8 1.0
CE1 A:PHE328 4.8 18.6 1.0
CZ A:PHE328 4.9 18.8 1.0
CD A:ARG307 4.9 14.9 1.0
OE2 A:GLU201 4.9 33.2 1.0

Iron binding site 2 out of 8 in 6qzo

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Iron binding site 2 out of 8 in the Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis


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 Dyp-Type Peroxidase From Cellulomonas Bogoriensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:17.9
occ:1.00
FE B:HEM401 0.0 17.9 1.0
ND B:HEM401 1.9 18.4 1.0
NA B:HEM401 2.0 18.1 1.0
NC B:HEM401 2.1 18.6 1.0
NB B:HEM401 2.1 17.8 1.0
NE2 B:HIS292 2.1 15.7 1.0
C1D B:HEM401 2.9 18.3 1.0
C4D B:HEM401 2.9 17.7 1.0
C1A B:HEM401 3.0 18.4 1.0
C4A B:HEM401 3.0 18.3 1.0
CD2 B:HIS292 3.1 16.2 1.0
C4B B:HEM401 3.1 17.8 1.0
C4C B:HEM401 3.1 18.8 1.0
C1B B:HEM401 3.1 17.6 1.0
C1C B:HEM401 3.1 18.9 1.0
CE1 B:HIS292 3.2 15.7 1.0
CHA B:HEM401 3.3 18.3 1.0
CHD B:HEM401 3.4 18.6 1.0
CHB B:HEM401 3.5 18.2 1.0
CHC B:HEM401 3.5 18.6 1.0
NH1 B:ARG307 4.1 14.6 1.0
C2D B:HEM401 4.1 18.5 1.0
C3D B:HEM401 4.2 18.4 1.0
C2A B:HEM401 4.2 18.6 1.0
C3A B:HEM401 4.2 18.3 1.0
CG B:HIS292 4.3 15.9 1.0
ND1 B:HIS292 4.3 15.5 1.0
C3C B:HEM401 4.3 19.8 1.0
C2C B:HEM401 4.3 18.9 1.0
C2B B:HEM401 4.3 17.5 1.0
C3B B:HEM401 4.4 17.8 1.0
OE1 B:GLU201 4.4 38.5 1.0
CE1 B:PHE328 4.8 15.7 1.0
CZ B:PHE328 4.9 15.5 1.0
CD B:ARG307 4.9 14.0 1.0
OE2 B:GLU201 4.9 32.6 1.0

Iron binding site 3 out of 8 in 6qzo

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Iron binding site 3 out of 8 in the Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis


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 Dyp-Type Peroxidase From Cellulomonas Bogoriensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:18.2
occ:1.00
FE C:HEM401 0.0 18.2 1.0
ND C:HEM401 1.9 19.3 1.0
NA C:HEM401 2.0 18.6 1.0
NE2 C:HIS292 2.1 15.7 1.0
NC C:HEM401 2.1 18.4 1.0
NB C:HEM401 2.1 18.8 1.0
C4D C:HEM401 2.9 18.4 1.0
C1D C:HEM401 2.9 18.4 1.0
C1A C:HEM401 3.0 18.9 1.0
CD2 C:HIS292 3.0 15.9 1.0
C4A C:HEM401 3.1 18.4 1.0
C1B C:HEM401 3.1 18.5 1.0
C4C C:HEM401 3.1 18.6 1.0
C4B C:HEM401 3.1 18.7 1.0
C1C C:HEM401 3.1 18.9 1.0
CE1 C:HIS292 3.1 15.6 1.0
CHA C:HEM401 3.3 19.4 1.0
CHD C:HEM401 3.4 18.5 1.0
CHB C:HEM401 3.5 18.4 1.0
CHC C:HEM401 3.5 19.0 1.0
C2D C:HEM401 4.2 18.4 1.0
C3D C:HEM401 4.2 18.4 1.0
CG C:HIS292 4.2 16.0 1.0
C2A C:HEM401 4.2 18.3 1.0
ND1 C:HIS292 4.2 15.7 1.0
C3A C:HEM401 4.2 18.2 1.0
C2C C:HEM401 4.3 19.1 1.0
NH2 C:ARG307 4.3 13.0 1.0
C3C C:HEM401 4.3 19.2 1.0
C2B C:HEM401 4.3 19.2 1.0
C3B C:HEM401 4.3 18.9 1.0
OE1 C:GLU201 4.4 30.5 1.0
CE1 C:PHE328 4.9 15.6 1.0
OE2 C:GLU201 4.9 30.1 1.0
CZ C:PHE328 4.9 15.9 1.0
CD C:ARG307 5.0 12.6 1.0

Iron binding site 4 out of 8 in 6qzo

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Iron binding site 4 out of 8 in the Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis


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 Dyp-Type Peroxidase From Cellulomonas Bogoriensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:25.4
occ:1.00
FE D:HEM401 0.0 25.4 1.0
ND D:HEM401 1.9 25.6 1.0
NA D:HEM401 2.0 25.0 1.0
NC D:HEM401 2.1 25.7 1.0
NE2 D:HIS292 2.1 24.4 1.0
NB D:HEM401 2.1 25.5 1.0
C4D D:HEM401 2.9 25.7 1.0
C1D D:HEM401 2.9 24.8 1.0
C1A D:HEM401 3.0 26.2 1.0
CD2 D:HIS292 3.0 24.6 1.0
C4A D:HEM401 3.0 25.6 1.0
C4C D:HEM401 3.1 25.9 1.0
C4B D:HEM401 3.1 24.5 1.0
C1C D:HEM401 3.1 25.6 1.0
C1B D:HEM401 3.1 24.4 1.0
CE1 D:HIS292 3.2 24.5 1.0
CHA D:HEM401 3.3 27.6 1.0
CHD D:HEM401 3.4 25.7 1.0
CHB D:HEM401 3.5 24.6 1.0
CHC D:HEM401 3.5 25.6 1.0
C2D D:HEM401 4.2 26.0 1.0
C3D D:HEM401 4.2 26.2 1.0
C2A D:HEM401 4.2 25.8 1.0
C3A D:HEM401 4.2 26.1 1.0
CG D:HIS292 4.2 24.4 1.0
NH2 D:ARG307 4.2 20.5 1.0
ND1 D:HIS292 4.3 24.2 1.0
C2C D:HEM401 4.3 25.5 1.0
C3C D:HEM401 4.3 26.2 1.0
OE1 D:GLU201 4.3 41.8 1.0
C2B D:HEM401 4.3 24.3 1.0
C3B D:HEM401 4.4 24.5 1.0
OE2 D:GLU201 4.9 39.2 1.0
CE1 D:PHE328 4.9 19.6 1.0
CD D:ARG307 5.0 20.0 1.0

Iron binding site 5 out of 8 in 6qzo

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Iron binding site 5 out of 8 in the Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis


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 Dyp-Type Peroxidase From Cellulomonas Bogoriensis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe401

b:20.4
occ:1.00
FE E:HEM401 0.0 20.4 1.0
ND E:HEM401 1.9 19.5 1.0
NA E:HEM401 2.0 19.2 1.0
NE2 E:HIS292 2.1 18.6 1.0
NC E:HEM401 2.1 18.9 1.0
NB E:HEM401 2.1 18.7 1.0
C4D E:HEM401 2.9 20.1 1.0
C1D E:HEM401 2.9 19.3 1.0
C1A E:HEM401 3.0 19.5 1.0
CD2 E:HIS292 3.0 18.5 1.0
C4A E:HEM401 3.1 19.5 1.0
C4C E:HEM401 3.1 19.1 1.0
C4B E:HEM401 3.1 18.8 1.0
C1B E:HEM401 3.1 19.1 1.0
C1C E:HEM401 3.1 19.0 1.0
CE1 E:HIS292 3.1 18.7 1.0
CHA E:HEM401 3.3 20.8 1.0
CHD E:HEM401 3.4 19.0 1.0
CHB E:HEM401 3.5 19.3 1.0
CHC E:HEM401 3.5 18.7 1.0
C2D E:HEM401 4.1 19.8 1.0
C3D E:HEM401 4.1 19.9 1.0
CG E:HIS292 4.2 18.2 1.0
ND1 E:HIS292 4.2 18.3 1.0
C2A E:HEM401 4.2 19.9 1.0
C3A E:HEM401 4.3 19.9 1.0
NH2 E:ARG307 4.3 15.1 1.0
C2C E:HEM401 4.3 18.8 1.0
C3C E:HEM401 4.3 19.5 1.0
C2B E:HEM401 4.3 18.7 1.0
C3B E:HEM401 4.4 18.5 1.0
OE1 E:GLU201 4.4 30.3 1.0
CE1 E:PHE328 4.9 18.0 1.0
CD E:ARG307 4.9 15.6 1.0
OE2 E:GLU201 4.9 29.2 1.0
CZ E:PHE328 4.9 18.0 1.0

Iron binding site 6 out of 8 in 6qzo

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Iron binding site 6 out of 8 in the Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis


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 Dyp-Type Peroxidase From Cellulomonas Bogoriensis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe401

b:25.3
occ:1.00
FE F:HEM401 0.0 25.3 1.0
ND F:HEM401 1.9 25.0 1.0
NA F:HEM401 2.0 24.3 1.0
NC F:HEM401 2.1 23.6 1.0
NB F:HEM401 2.1 24.6 1.0
NE2 F:HIS292 2.1 26.1 1.0
C1D F:HEM401 2.9 25.2 1.0
C4D F:HEM401 2.9 25.7 1.0
C1A F:HEM401 3.0 25.7 1.0
C4C F:HEM401 3.0 23.7 1.0
C4A F:HEM401 3.0 25.1 1.0
CD2 F:HIS292 3.1 26.3 1.0
C4B F:HEM401 3.1 24.5 1.0
C1B F:HEM401 3.1 24.1 1.0
C1C F:HEM401 3.1 23.9 1.0
CE1 F:HIS292 3.2 26.4 1.0
CHA F:HEM401 3.3 26.4 1.0
CHD F:HEM401 3.3 24.1 1.0
CHB F:HEM401 3.5 24.4 1.0
CHC F:HEM401 3.5 24.2 1.0
NH1 F:ARG307 4.1 23.5 1.0
C2D F:HEM401 4.1 26.4 1.0
C3D F:HEM401 4.1 26.8 1.0
C2A F:HEM401 4.2 25.6 1.0
C3A F:HEM401 4.2 25.2 1.0
CG F:HIS292 4.2 26.6 1.0
ND1 F:HIS292 4.3 26.7 1.0
C3C F:HEM401 4.3 23.6 1.0
C2C F:HEM401 4.3 23.3 1.0
C2B F:HEM401 4.3 24.3 1.0
C3B F:HEM401 4.4 23.7 1.0
OE1 F:GLU201 4.4 34.5 1.0
CE1 F:PHE328 4.8 26.3 1.0
CD F:ARG307 4.9 23.6 1.0
OE2 F:GLU201 4.9 33.2 1.0
CZ F:PHE328 4.9 26.4 1.0
CZ F:ARG307 5.0 23.5 1.0

Iron binding site 7 out of 8 in 6qzo

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Iron binding site 7 out of 8 in the Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe401

b:26.5
occ:1.00
FE G:HEM401 0.0 26.5 1.0
ND G:HEM401 1.9 25.1 1.0
NA G:HEM401 2.0 25.2 1.0
NE2 G:HIS292 2.1 33.6 1.0
NC G:HEM401 2.1 23.8 1.0
NB G:HEM401 2.1 24.6 1.0
C1D G:HEM401 2.9 25.0 1.0
C4D G:HEM401 2.9 25.9 1.0
C1A G:HEM401 3.0 25.3 1.0
CD2 G:HIS292 3.0 33.3 1.0
C4A G:HEM401 3.0 25.1 1.0
C4C G:HEM401 3.0 23.9 1.0
C1B G:HEM401 3.1 24.8 1.0
C4B G:HEM401 3.1 24.8 1.0
C1C G:HEM401 3.1 23.7 1.0
CE1 G:HIS292 3.1 33.7 1.0
CHD G:HEM401 3.3 23.7 1.0
CHA G:HEM401 3.3 26.1 1.0
CHB G:HEM401 3.4 25.0 1.0
CHC G:HEM401 3.5 24.1 1.0
NH1 G:ARG307 4.1 31.7 1.0
C2D G:HEM401 4.1 26.1 1.0
C3D G:HEM401 4.1 26.9 1.0
CG G:HIS292 4.2 33.3 1.0
C2A G:HEM401 4.2 25.4 1.0
ND1 G:HIS292 4.2 33.8 1.0
C3A G:HEM401 4.2 25.0 1.0
C3C G:HEM401 4.3 24.9 1.0
C2C G:HEM401 4.3 23.4 1.0
C2B G:HEM401 4.3 24.6 1.0
C3B G:HEM401 4.4 23.8 1.0
OE1 G:GLU201 4.5 31.6 1.0
OE2 G:GLU201 4.9 31.9 1.0
CD G:ARG307 4.9 30.7 1.0
CE1 G:PHE328 4.9 25.6 1.0
CZ G:ARG307 4.9 32.0 1.0
CZ G:PHE328 5.0 25.7 1.0

Iron binding site 8 out of 8 in 6qzo

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Iron binding site 8 out of 8 in the Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Dyp-Type Peroxidase From Cellulomonas Bogoriensis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe401

b:16.6
occ:1.00
FE H:HEM401 0.0 16.6 1.0
ND H:HEM401 1.9 16.6 1.0
NA H:HEM401 2.0 15.9 1.0
NC H:HEM401 2.1 16.2 1.0
NE2 H:HIS292 2.1 18.9 1.0
NB H:HEM401 2.1 16.3 1.0
C1D H:HEM401 2.9 16.6 1.0
C4D H:HEM401 2.9 16.9 1.0
C1A H:HEM401 3.0 16.3 1.0
CD2 H:HIS292 3.0 19.1 1.0
C4A H:HEM401 3.0 15.8 1.0
C4C H:HEM401 3.0 16.1 1.0
C1B H:HEM401 3.1 16.1 1.0
C4B H:HEM401 3.1 16.4 1.0
C1C H:HEM401 3.1 16.4 1.0
CE1 H:HIS292 3.2 19.4 1.0
CHD H:HEM401 3.4 16.1 1.0
CHA H:HEM401 3.4 16.8 1.0
CHB H:HEM401 3.4 15.9 1.0
CHC H:HEM401 3.5 16.3 1.0
NH2 H:ARG307 4.2 18.5 1.0
C2D H:HEM401 4.2 17.4 1.0
C3A H:HEM401 4.2 16.0 1.0
C2A H:HEM401 4.2 16.3 1.0
CG H:HIS292 4.2 19.3 1.0
C3D H:HEM401 4.2 17.4 1.0
ND1 H:HIS292 4.2 19.2 1.0
C3C H:HEM401 4.3 15.9 1.0
C2C H:HEM401 4.3 16.1 1.0
OE1 H:GLU201 4.3 27.1 1.0
C2B H:HEM401 4.3 16.2 1.0
C3B H:HEM401 4.4 16.2 1.0
CE1 H:PHE328 4.9 15.8 1.0
OE2 H:GLU201 4.9 26.4 1.0
CD H:ARG307 4.9 18.2 1.0
CZ H:ARG307 5.0 18.2 1.0
CZ H:PHE328 5.0 15.8 1.0
CD H:GLU201 5.0 25.6 1.0

Reference:

M.H.Habib, H.J.Rozeboom, M.W.Fraaije. Characterization of A New Dyp-Peroxidase From the Alkaliphilic Cellulomonad, Cellulomonas Bogoriensis. Molecules V. 24 2019.
ISSN: ESSN 1420-3049
PubMed: 30934796
DOI: 10.3390/MOLECULES24071208
Page generated: Wed Aug 7 08:20:01 2024

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