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Iron in PDB 5vj0: Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus

Protein crystallography data

The structure of Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus, PDB code: 5vj0 was solved by D.A.Meekins, P.Li, B.V.Geisbrecht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.45 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.870, 74.160, 118.640, 90.00, 108.17, 90.00
R / Rfree (%) 17.3 / 20.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus (pdb code 5vj0). 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 of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus, PDB code: 5vj0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5vj0

Go back to Iron Binding Sites List in 5vj0
Iron binding site 1 out of 4 in the Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus


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 Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:24.7
occ:1.00
FE A:HEM500 0.0 24.7 1.0
ND A:HEM500 2.0 17.7 1.0
NB A:HEM500 2.0 21.5 1.0
NA A:HEM500 2.0 22.8 1.0
NC A:HEM500 2.0 25.1 1.0
NE2 A:HIS215 2.2 21.3 1.0
C4B A:HEM500 3.0 23.6 1.0
C4D A:HEM500 3.0 22.6 1.0
C1A A:HEM500 3.0 23.5 1.0
C1C A:HEM500 3.1 21.2 1.0
C1D A:HEM500 3.1 23.6 1.0
C4C A:HEM500 3.1 19.8 1.0
C4A A:HEM500 3.1 22.7 1.0
C1B A:HEM500 3.1 21.0 1.0
CD2 A:HIS215 3.2 22.9 1.0
CE1 A:HIS215 3.2 21.0 1.0
CHC A:HEM500 3.4 20.2 1.0
CHA A:HEM500 3.4 20.2 1.0
CHD A:HEM500 3.4 24.1 1.0
CHB A:HEM500 3.5 25.1 1.0
NH1 A:ARG232 4.2 22.0 1.0
C3B A:HEM500 4.2 23.1 1.0
C2A A:HEM500 4.3 22.6 1.0
C3D A:HEM500 4.3 22.9 1.0
C3C A:HEM500 4.3 21.1 1.0
C2B A:HEM500 4.3 21.0 1.0
C2D A:HEM500 4.3 21.9 1.0
C2C A:HEM500 4.3 22.7 1.0
C3A A:HEM500 4.3 22.3 1.0
CG A:HIS215 4.3 24.1 1.0
ND1 A:HIS215 4.3 21.2 1.0
CE1 A:PHE248 4.7 18.3 1.0
CD A:ARG232 4.7 20.3 1.0
OD1 A:ASP143 4.8 32.4 1.0
CE A:MET276 4.8 21.2 1.0
CZ A:ARG232 4.8 22.9 1.0

Iron binding site 2 out of 4 in 5vj0

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Iron binding site 2 out of 4 in the Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus


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 Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:28.7
occ:1.00
FE B:HEM500 0.0 28.7 1.0
NC B:HEM500 2.0 23.3 1.0
NA B:HEM500 2.0 21.1 1.0
NB B:HEM500 2.1 25.5 1.0
ND B:HEM500 2.1 25.7 1.0
NE2 B:HIS215 2.3 24.2 1.0
C4C B:HEM500 3.0 28.3 1.0
C4A B:HEM500 3.0 25.1 1.0
C1C B:HEM500 3.0 28.4 1.0
C1D B:HEM500 3.1 27.2 1.0
C1B B:HEM500 3.1 26.3 1.0
C4B B:HEM500 3.1 28.9 1.0
C1A B:HEM500 3.1 24.4 1.0
C4D B:HEM500 3.1 26.7 1.0
CD2 B:HIS215 3.1 24.3 1.0
O B:HOH614 3.2 32.8 1.0
CE1 B:HIS215 3.3 24.6 1.0
CHD B:HEM500 3.4 28.5 1.0
CHB B:HEM500 3.4 26.7 1.0
CHC B:HEM500 3.4 27.8 1.0
CHA B:HEM500 3.5 26.3 1.0
C3C B:HEM500 4.2 26.6 1.0
C2C B:HEM500 4.2 26.0 1.0
C3A B:HEM500 4.3 25.6 1.0
NH1 B:ARG232 4.3 27.8 1.0
C2A B:HEM500 4.3 23.7 1.0
C2D B:HEM500 4.3 30.1 1.0
C2B B:HEM500 4.3 24.3 1.0
C3B B:HEM500 4.3 26.9 1.0
C3D B:HEM500 4.3 28.6 1.0
CG B:HIS215 4.3 26.4 1.0
ND1 B:HIS215 4.4 28.0 1.0
CE1 B:PHE248 4.5 27.2 1.0
CD B:ARG232 4.6 26.1 1.0
OD1 B:ASP143 4.8 32.9 1.0
CZ B:ARG232 4.8 28.1 1.0
CE B:MET276 4.9 26.2 1.0
NE B:ARG232 5.0 25.8 1.0

Iron binding site 3 out of 4 in 5vj0

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Iron binding site 3 out of 4 in the Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus


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 Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:17.2
occ:1.00
FE C:HEM500 0.0 17.2 1.0
NC C:HEM500 2.0 17.0 1.0
ND C:HEM500 2.1 15.5 1.0
NA C:HEM500 2.1 17.5 1.0
NB C:HEM500 2.1 15.6 1.0
NE2 C:HIS215 2.2 14.4 1.0
C4A C:HEM500 3.0 17.2 1.0
C4C C:HEM500 3.0 17.4 1.0
C1D C:HEM500 3.0 15.4 1.0
C1B C:HEM500 3.1 16.8 1.0
C1C C:HEM500 3.1 18.1 1.0
C4D C:HEM500 3.1 17.9 1.0
C4B C:HEM500 3.1 17.2 1.0
C1A C:HEM500 3.1 16.8 1.0
CD2 C:HIS215 3.2 15.5 1.0
CE1 C:HIS215 3.2 15.6 1.0
CHB C:HEM500 3.4 18.2 1.0
CHD C:HEM500 3.4 16.9 1.0
CHC C:HEM500 3.5 16.5 1.0
CHA C:HEM500 3.5 16.8 1.0
NH1 C:ARG232 4.2 16.2 1.0
C3C C:HEM500 4.3 16.5 1.0
C3A C:HEM500 4.3 18.1 1.0
C2C C:HEM500 4.3 17.7 1.0
C2D C:HEM500 4.3 17.7 1.0
C2A C:HEM500 4.3 17.1 1.0
C2B C:HEM500 4.3 18.7 1.0
C3D C:HEM500 4.3 18.4 1.0
ND1 C:HIS215 4.3 15.3 1.0
C3B C:HEM500 4.3 18.4 1.0
CG C:HIS215 4.3 16.5 1.0
O C:HOH765 4.5 22.4 1.0
CD C:ARG232 4.7 15.2 1.0
CE1 C:PHE248 4.7 15.9 1.0
CE C:MET276 4.7 19.6 1.0
CZ C:ARG232 4.9 16.3 1.0

Iron binding site 4 out of 4 in 5vj0

Go back to Iron Binding Sites List in 5vj0
Iron binding site 4 out of 4 in the Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus


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 Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe500

b:28.6
occ:1.00
FE D:HEM500 0.0 28.6 1.0
NC D:HEM500 2.0 23.8 1.0
NA D:HEM500 2.0 26.9 1.0
ND D:HEM500 2.0 25.6 1.0
NB D:HEM500 2.1 26.5 1.0
NE2 D:HIS215 2.3 21.1 1.0
C4C D:HEM500 3.0 26.5 1.0
C4A D:HEM500 3.0 26.8 1.0
C1D D:HEM500 3.0 24.6 1.0
C1A D:HEM500 3.1 29.4 1.0
C1C D:HEM500 3.1 25.5 1.0
C1B D:HEM500 3.1 26.2 1.0
C4D D:HEM500 3.1 26.5 1.0
CD2 D:HIS215 3.1 26.0 1.0
C4B D:HEM500 3.1 21.5 1.0
CHD D:HEM500 3.4 25.8 1.0
CHB D:HEM500 3.4 28.1 1.0
CE1 D:HIS215 3.4 26.0 1.0
CHA D:HEM500 3.5 27.5 1.0
CHC D:HEM500 3.5 23.4 1.0
NH1 D:ARG232 4.1 28.6 1.0
C3A D:HEM500 4.2 28.0 1.0
C3C D:HEM500 4.2 25.6 1.0
C2A D:HEM500 4.2 29.1 1.0
C2C D:HEM500 4.3 22.8 1.0
C2D D:HEM500 4.3 27.0 1.0
C3D D:HEM500 4.3 27.2 1.0
C2B D:HEM500 4.3 24.2 1.0
C3B D:HEM500 4.3 25.4 1.0
CG D:HIS215 4.3 26.2 1.0
ND1 D:HIS215 4.4 26.0 1.0
CE2 D:PHE248 4.7 21.6 1.0
CD D:ARG232 4.8 25.7 1.0
OD1 D:ASP143 4.9 35.1 1.0
CZ D:ARG232 4.9 30.4 1.0

Reference:

R.Shrestha, G.Huang, D.A.Meekins, B.V.Geisbrecht, P.Li. Mechanistic Insights Into Dye-Decolorizing Peroxidase Revealed By Solvent Isotope and Viscosity Effects. Acs Catal V. 7 6352 2017.
ISSN: ESSN 2155-5435
PubMed: 29308295
DOI: 10.1021/ACSCATAL.7B01861
Page generated: Tue Aug 6 10:26:27 2024

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