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Iron in PDB 4gu7: Crystal Structure of Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor

Enzymatic activity of Crystal Structure of Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor

All present enzymatic activity of Crystal Structure of Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor:
1.11.1.19;

Protein crystallography data

The structure of Crystal Structure of Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor, PDB code: 4gu7 was solved by T.Lukk, A.M.A.Hetta, A.Jones, J.Solbiati, S.Majumdar, J.E.Cronan, J.A.Gerlt, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.49 / 3.10
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 188.950, 188.950, 188.950, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 20.3

Other elements in 4gu7:

The structure of Crystal Structure of Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor (pdb code 4gu7). 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 Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor, PDB code: 4gu7:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4gu7

Go back to Iron Binding Sites List in 4gu7
Iron binding site 1 out of 4 in the Crystal Structure of Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor


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 (SCO7193) From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:43.0
occ:1.00
 FE A:HEM401 0.0 43.0 1.0
ND A:HEM401 2.0 42.5 1.0
NA A:HEM401 2.0 47.2 1.0
NB A:HEM401 2.1 41.3 1.0
NC A:HEM401 2.1 42.4 1.0
NE2 A:HIS225 2.3 41.6 1.0
C4D A:HEM401 2.9 42.4 1.0
C1A A:HEM401 3.0 45.7 1.0
C1D A:HEM401 3.1 41.1 1.0
C4A A:HEM401 3.1 47.4 1.0
C4B A:HEM401 3.1 41.7 1.0
C1C A:HEM401 3.1 44.7 1.0
C1B A:HEM401 3.1 44.5 1.0
C4C A:HEM401 3.2 37.7 1.0
CE1 A:HIS225 3.2 45.3 1.0
CD2 A:HIS225 3.3 45.5 1.0
CHA A:HEM401 3.3 41.3 1.0
CHC A:HEM401 3.5 42.3 1.0
CHD A:HEM401 3.5 38.1 1.0
CHB A:HEM401 3.5 48.6 1.0
NE A:ARG243 4.0 48.8 1.0
ND2 A:ASN245 4.2 50.7 1.0
C3D A:HEM401 4.2 41.0 1.0
C2A A:HEM401 4.2 45.5 1.0
C2D A:HEM401 4.3 41.1 1.0
C3A A:HEM401 4.3 41.6 1.0
CD A:ARG243 4.3 49.5 1.0
C3B A:HEM401 4.3 39.5 1.0
ND1 A:HIS225 4.4 50.8 1.0
C2B A:HEM401 4.4 43.5 1.0
C2C A:HEM401 4.4 44.1 1.0
C3C A:HEM401 4.4 39.8 1.0
CG A:HIS225 4.4 47.6 1.0
CZ A:ARG243 4.7 46.2 1.0

Iron binding site 2 out of 4 in 4gu7

Go back to Iron Binding Sites List in 4gu7
Iron binding site 2 out of 4 in the Crystal Structure of Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor


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 (SCO7193) From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:40.3
occ:1.00
 FE B:HEM401 0.0 40.3 1.0
NA B:HEM401 2.0 45.7 1.0
ND B:HEM401 2.1 42.5 1.0
NB B:HEM401 2.1 42.1 1.0
NC B:HEM401 2.2 39.3 1.0
NE2 B:HIS225 2.3 35.5 1.0
C1A B:HEM401 3.0 44.7 1.0
C4D B:HEM401 3.0 40.2 1.0
C4A B:HEM401 3.0 49.0 1.0
C4B B:HEM401 3.1 38.8 1.0
C1C B:HEM401 3.1 38.3 1.0
C1B B:HEM401 3.1 42.9 1.0
CD2 B:HIS225 3.2 42.5 1.0
C1D B:HEM401 3.2 42.9 1.0
CHA B:HEM401 3.3 43.3 1.0
C4C B:HEM401 3.3 35.4 1.0
CE1 B:HIS225 3.3 40.3 1.0
CHC B:HEM401 3.4 35.7 1.0
CHB B:HEM401 3.5 44.6 1.0
CHD B:HEM401 3.6 35.6 1.0
NE B:ARG243 4.1 47.1 1.0
C2A B:HEM401 4.2 44.9 1.0
C3A B:HEM401 4.2 48.7 1.0
C3D B:HEM401 4.3 39.8 1.0
C3B B:HEM401 4.3 42.0 1.0
CD B:ARG243 4.3 41.7 1.0
C2B B:HEM401 4.3 41.1 1.0
CG B:HIS225 4.4 41.0 1.0
ND2 B:ASN245 4.4 45.5 1.0
C2C B:HEM401 4.4 42.5 1.0
C2D B:HEM401 4.4 41.5 1.0
ND1 B:HIS225 4.4 44.4 1.0
C3C B:HEM401 4.5 40.2 1.0
CZ B:ARG243 4.7 48.9 1.0

Iron binding site 3 out of 4 in 4gu7

Go back to Iron Binding Sites List in 4gu7
Iron binding site 3 out of 4 in the Crystal Structure of Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor


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 (SCO7193) From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:41.3
occ:1.00
 FE C:HEM401 0.0 41.3 1.0
NA C:HEM401 2.0 46.0 1.0
ND C:HEM401 2.1 45.5 1.0
NB C:HEM401 2.1 42.5 1.0
NC C:HEM401 2.1 43.2 1.0
NE2 C:HIS225 2.4 39.8 1.0
C1A C:HEM401 3.0 44.1 1.0
C4D C:HEM401 3.0 42.5 1.0
C4A C:HEM401 3.1 45.7 1.0
C1D C:HEM401 3.1 42.4 1.0
C1C C:HEM401 3.1 44.9 1.0
C4B C:HEM401 3.1 40.8 1.0
C1B C:HEM401 3.1 43.9 1.0
C4C C:HEM401 3.2 44.1 1.0
CD2 C:HIS225 3.2 42.6 1.0
CHA C:HEM401 3.3 43.6 1.0
CE1 C:HIS225 3.4 43.9 1.0
CHC C:HEM401 3.5 41.5 1.0
CHB C:HEM401 3.5 44.3 1.0
CHD C:HEM401 3.5 41.9 1.0
NE C:ARG243 3.9 47.4 1.0
CD C:ARG243 4.1 44.8 1.0
ND2 C:ASN245 4.1 47.9 1.0
C3A C:HEM401 4.3 43.4 1.0
C2A C:HEM401 4.3 42.2 1.0
C3D C:HEM401 4.3 40.3 1.0
C2D C:HEM401 4.3 39.6 1.0
C3B C:HEM401 4.3 42.4 1.0
C2C C:HEM401 4.3 47.2 1.0
C2B C:HEM401 4.4 43.9 1.0
C3C C:HEM401 4.4 47.0 1.0
CG C:HIS225 4.4 49.2 1.0
ND1 C:HIS225 4.5 48.7 1.0
CZ C:ARG243 4.7 49.3 1.0

Iron binding site 4 out of 4 in 4gu7

Go back to Iron Binding Sites List in 4gu7
Iron binding site 4 out of 4 in the Crystal Structure of Dyp-Type Peroxidase (SCO7193) From Streptomyces Coelicolor


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 (SCO7193) From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:41.4
occ:1.00
 FE D:HEM401 0.0 41.4 1.0
NA D:HEM401 2.0 46.2 1.0
NB D:HEM401 2.1 36.0 1.0
ND D:HEM401 2.1 38.7 1.0
NC D:HEM401 2.1 39.6 1.0
NE2 D:HIS225 2.4 40.1 1.0
C1A D:HEM401 3.0 41.8 1.0
C4D D:HEM401 3.0 37.6 1.0
C4A D:HEM401 3.1 46.5 1.0
C4B D:HEM401 3.1 36.8 1.0
C1C D:HEM401 3.1 40.5 1.0
C1B D:HEM401 3.1 39.4 1.0
C1D D:HEM401 3.1 40.5 1.0
C4C D:HEM401 3.2 41.3 1.0
CE1 D:HIS225 3.2 42.1 1.0
CD2 D:HIS225 3.3 41.0 1.0
CHA D:HEM401 3.3 38.9 1.0
CHC D:HEM401 3.4 41.2 1.0
CHB D:HEM401 3.5 41.8 1.0
CHD D:HEM401 3.5 41.8 1.0
NE D:ARG243 4.0 49.5 1.0
CD D:ARG243 4.2 44.9 1.0
C3A D:HEM401 4.3 42.5 1.0
C2A D:HEM401 4.3 42.1 1.0
ND1 D:HIS225 4.3 47.3 1.0
C3B D:HEM401 4.3 39.7 1.0
C3D D:HEM401 4.3 38.3 1.0
C2B D:HEM401 4.3 41.6 1.0
CG D:HIS225 4.3 42.1 1.0
C2C D:HEM401 4.4 38.2 1.0
C2D D:HEM401 4.4 40.4 1.0
C3C D:HEM401 4.4 40.3 1.0
ND2 D:ASN245 4.5 49.5 1.0
CZ D:ARG243 4.8 48.8 1.0

Reference:

T.Lukk, A.M.A.Hetta, A.Jones, J.Solbiati, S.Majumdar, J.E.Cronan, J.A.Gerlt, S.K.Nair. Dyp-Type Peroxidases From Stretptomyces and Thermobifida Can Modify Organosolv Lignin. To Be Published.
Page generated: Mon Aug 5 03:04:59 2024

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