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Iron in PDB 4b31: Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum

Enzymatic activity of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum

All present enzymatic activity of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum:
1.11.1.6;

Protein crystallography data

The structure of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum, PDB code: 4b31 was solved by Y.Yuzugullu, C.H.Trinh, A.R.Pearson, Z.B.Ogel, M.J.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 113.27 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.045, 121.310, 125.589, 90.00, 115.58, 90.00
R / Rfree (%) 15.15 / 20.845

Other elements in 4b31:

The structure of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum also contains other interesting chemical elements:

Calcium (Ca) 5 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum (pdb code 4b31). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum, PDB code: 4b31:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4b31

Go back to Iron Binding Sites List in 4b31
Iron binding site 1 out of 4 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe900

b:10.3
occ:1.00
 FE A:HDD900 0.0 10.3 1.0
OH A:TYR369 1.9 6.3 1.0
ND A:HDD900 2.0 11.0 1.0
NC A:HDD900 2.1 11.0 1.0
NA A:HDD900 2.1 10.1 1.0
NB A:HDD900 2.1 11.2 1.0
O A:HOH2098 2.9 7.3 0.3
C1D A:HDD900 3.0 11.4 1.0
CZ A:TYR369 3.0 6.7 1.0
C4C A:HDD900 3.0 11.0 1.0
C4D A:HDD900 3.0 10.7 1.0
C1A A:HDD900 3.1 9.9 1.0
C4B A:HDD900 3.1 11.2 1.0
C4A A:HDD900 3.1 10.2 1.0
C1C A:HDD900 3.1 10.9 1.0
C1B A:HDD900 3.1 11.3 1.0
CHD A:HDD900 3.3 10.7 1.0
CHA A:HDD900 3.4 9.8 1.0
CHB A:HDD900 3.5 10.7 1.0
CHC A:HDD900 3.5 10.9 1.0
CE1 A:TYR369 3.8 6.7 1.0
CE2 A:TYR369 3.8 6.7 1.0
NE A:ARG365 4.1 9.9 1.0
NH2 A:ARG365 4.2 10.4 1.0
C3C A:HDD900 4.3 10.4 1.0
C2D A:HDD900 4.3 11.9 1.0
C3D A:HDD900 4.4 11.8 1.0
C2A A:HDD900 4.4 9.2 1.0
CZ A:PHE168 4.4 7.2 1.0
C2C A:HDD900 4.4 10.6 1.0
C3B A:HDD900 4.4 11.7 1.0
C3A A:HDD900 4.4 9.6 1.0
C2B A:HDD900 4.5 11.5 1.0
CZ A:ARG365 4.6 10.5 1.0
CG2 A:VAL81 4.6 6.9 1.0
O A:HOH2096 4.7 20.5 1.0
NE2 A:HIS82 4.9 9.9 1.0
CE2 A:PHE168 4.9 7.2 1.0
CD2 A:HIS82 4.9 8.9 1.0
CE1 A:PHE168 5.0 7.4 1.0

Iron binding site 2 out of 4 in 4b31

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Iron binding site 2 out of 4 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe900

b:10.9
occ:1.00
 FE B:HDD900 0.0 10.9 1.0
OH B:TYR369 1.9 6.8 1.0
ND B:HDD900 2.0 11.8 1.0
NC B:HDD900 2.1 11.6 1.0
NA B:HDD900 2.1 10.8 1.0
NB B:HDD900 2.1 11.6 1.0
C1D B:HDD900 3.0 11.7 1.0
CZ B:TYR369 3.0 7.0 1.0
C4D B:HDD900 3.0 11.4 1.0
C4C B:HDD900 3.0 10.8 1.0
O B:HOH2074 3.1 19.2 0.3
C4A B:HDD900 3.1 10.9 1.0
C1A B:HDD900 3.1 10.8 1.0
C4B B:HDD900 3.1 11.9 1.0
C1B B:HDD900 3.1 11.4 1.0
C1C B:HDD900 3.2 10.7 1.0
CHD B:HDD900 3.3 11.1 1.0
CHA B:HDD900 3.4 10.6 1.0
CHB B:HDD900 3.4 11.0 1.0
CHC B:HDD900 3.6 10.8 1.0
CE2 B:TYR369 3.7 7.2 1.0
CE1 B:TYR369 3.8 7.4 1.0
NE B:ARG365 4.1 9.6 1.0
NH2 B:ARG365 4.1 9.0 1.0
C3C B:HDD900 4.3 10.0 1.0
C2D B:HDD900 4.3 12.8 1.0
C3D B:HDD900 4.3 12.5 1.0
C3A B:HDD900 4.4 10.6 1.0
C2A B:HDD900 4.4 10.0 1.0
C2C B:HDD900 4.4 10.2 1.0
C3B B:HDD900 4.4 12.1 1.0
C2B B:HDD900 4.5 11.8 1.0
CZ B:ARG365 4.5 9.3 1.0
NE2 B:HIS82 4.6 7.5 1.0
CG2 B:VAL81 4.6 6.0 1.0
CZ B:PHE168 4.7 7.0 1.0
CD2 B:HIS82 4.7 6.9 1.0
O B:HOH2075 4.8 29.6 1.0
CD2 B:TYR369 4.9 7.2 1.0

Iron binding site 3 out of 4 in 4b31

Go back to Iron Binding Sites List in 4b31
Iron binding site 3 out of 4 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe900

b:9.2
occ:1.00
 FE C:HDD900 0.0 9.2 1.0
OH C:TYR369 1.9 6.5 1.0
ND C:HDD900 2.0 9.8 1.0
NC C:HDD900 2.0 9.3 1.0
NB C:HDD900 2.1 9.4 1.0
NA C:HDD900 2.1 8.9 1.0
CZ C:TYR369 2.9 7.1 1.0
O C:HOH2024 3.0 10.9 0.3
C1D C:HDD900 3.0 10.0 1.0
C4D C:HDD900 3.0 10.0 1.0
C4C C:HDD900 3.0 9.4 1.0
C1C C:HDD900 3.1 9.3 1.0
C4B C:HDD900 3.1 9.4 1.0
C4A C:HDD900 3.1 8.5 1.0
C1B C:HDD900 3.1 9.3 1.0
C1A C:HDD900 3.1 9.0 1.0
CHD C:HDD900 3.4 9.2 1.0
CHB C:HDD900 3.4 8.8 1.0
CHC C:HDD900 3.4 9.0 1.0
CHA C:HDD900 3.5 9.0 1.0
CE2 C:TYR369 3.6 7.2 1.0
CE1 C:TYR369 3.8 7.0 1.0
NE C:ARG365 4.1 9.3 1.0
NH2 C:ARG365 4.2 9.0 1.0
C3C C:HDD900 4.3 9.2 1.0
C3D C:HDD900 4.4 10.7 1.0
C3B C:HDD900 4.4 9.4 1.0
C2D C:HDD900 4.4 10.3 1.0
C3A C:HDD900 4.4 8.6 1.0
C2C C:HDD900 4.4 9.2 1.0
C2A C:HDD900 4.4 8.4 1.0
C2B C:HDD900 4.5 9.3 1.0
CZ C:PHE168 4.5 7.4 1.0
CZ C:ARG365 4.6 9.0 1.0
CG2 C:VAL81 4.7 6.3 1.0
NE2 C:HIS82 4.8 11.2 1.0
CD2 C:HIS82 4.8 9.8 1.0
O C:HOH2023 4.9 21.6 1.0
CD2 C:TYR369 4.9 7.4 1.0
CE2 C:PHE168 4.9 7.4 1.0

Iron binding site 4 out of 4 in 4b31

Go back to Iron Binding Sites List in 4b31
Iron binding site 4 out of 4 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe900

b:10.6
occ:1.00
 FE D:HDD900 0.0 10.6 1.0
OH D:TYR369 2.0 6.2 1.0
ND D:HDD900 2.0 11.0 1.0
NC D:HDD900 2.1 9.9 1.0
NB D:HDD900 2.1 10.9 1.0
NA D:HDD900 2.1 10.6 1.0
C1D D:HDD900 3.0 11.1 1.0
C4D D:HDD900 3.0 11.4 1.0
CZ D:TYR369 3.0 6.2 1.0
C4C D:HDD900 3.0 10.0 1.0
C4B D:HDD900 3.1 10.8 1.0
C1A D:HDD900 3.1 10.3 1.0
C4A D:HDD900 3.1 10.4 1.0
C1C D:HDD900 3.1 10.0 1.0
C1B D:HDD900 3.1 10.7 1.0
O D:HOH2023 3.2 15.1 0.3
CHD D:HDD900 3.4 10.6 1.0
CHA D:HDD900 3.4 10.2 1.0
CHC D:HDD900 3.4 10.1 1.0
CHB D:HDD900 3.5 10.7 1.0
CE2 D:TYR369 3.7 6.2 1.0
CE1 D:TYR369 3.9 6.2 1.0
NH2 D:ARG365 4.1 8.7 1.0
NE D:ARG365 4.2 8.5 1.0
C2D D:HDD900 4.3 12.4 1.0
C3D D:HDD900 4.3 12.2 1.0
C3C D:HDD900 4.3 9.7 1.0
C3B D:HDD900 4.4 10.9 1.0
C2A D:HDD900 4.4 10.0 1.0
C3A D:HDD900 4.4 10.4 1.0
C2C D:HDD900 4.4 9.7 1.0
C2B D:HDD900 4.4 11.1 1.0
CZ D:PHE168 4.5 7.9 1.0
CG2 D:VAL81 4.6 6.7 1.0
CZ D:ARG365 4.6 8.8 1.0
CD2 D:HIS82 4.7 8.5 1.0
NE2 D:HIS82 4.7 9.5 1.0
CD2 D:TYR369 4.9 6.0 1.0
CE2 D:PHE168 5.0 7.7 1.0
OND D:HDD900 5.0 14.0 1.0

Reference:

Y.Yuzugullu, C.H.Trinh, L.Fairhurst, Z.B.Ogel, M.J.Mcpherson, A.R.Pearson. Investigating the Active Centre of the Scytalidium Thermophilum Catalase Acta Crystallogr.,Sect.F V. 69 369 2013.
ISSN: ISSN 1744-3091
PubMed: 23545640
DOI: 10.1107/S1744309113004211
Page generated: Sun Aug 4 23:56:42 2024

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