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Iron in PDB 4b5k: 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: 4b5k 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) 28.92 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.392, 122.000, 125.670, 90.00, 115.48, 90.00
R / Rfree (%) 15.298 / 18.041

Other elements in 4b5k:

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

Calcium (Ca) 9 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 4b5k). 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: 4b5k:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4b5k

Go back to Iron Binding Sites List in 4b5k
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:14.3
occ:1.00
 FE A:HDD900 0.0 14.3 1.0
ND A:HDD900 2.0 13.4 1.0
OH A:TYR369 2.0 12.7 1.0
NA A:HDD900 2.0 12.6 1.0
NC A:HDD900 2.1 13.0 1.0
NB A:HDD900 2.1 14.0 1.0
O A:HOH2106 2.4 14.5 0.3
CZ A:TYR369 3.0 12.4 1.0
C4D A:HDD900 3.0 13.2 1.0
C4A A:HDD900 3.0 12.3 1.0
C1D A:HDD900 3.0 14.2 1.0
C1A A:HDD900 3.1 12.7 1.0
C4C A:HDD900 3.1 13.2 1.0
C1C A:HDD900 3.1 13.2 1.0
C4B A:HDD900 3.1 13.3 1.0
C1B A:HDD900 3.1 13.2 1.0
CHA A:HDD900 3.4 12.6 1.0
CHB A:HDD900 3.4 12.5 1.0
CHD A:HDD900 3.4 13.7 1.0
CHC A:HDD900 3.5 13.3 1.0
CE2 A:TYR369 3.8 12.2 1.0
CE1 A:TYR369 3.8 12.3 1.0
NE A:ARG365 4.1 12.1 1.0
NH2 A:ARG365 4.2 11.9 1.0
O A:HOH2104 4.3 27.7 1.0
C2A A:HDD900 4.3 11.4 1.0
C3A A:HDD900 4.3 10.9 1.0
C3C A:HDD900 4.4 13.1 1.0
C3B A:HDD900 4.4 13.8 1.0
C3D A:HDD900 4.4 14.1 1.0
C2C A:HDD900 4.4 12.8 1.0
C2D A:HDD900 4.4 14.5 1.0
C2B A:HDD900 4.4 12.8 1.0
CG2 A:VAL81 4.5 13.3 1.0
CZ A:ARG365 4.6 12.4 1.0
CZ A:PHE168 4.6 14.3 1.0
CD2 A:HIS82 4.8 12.8 1.0
NE2 A:HIS82 4.9 12.6 1.0

Iron binding site 2 out of 4 in 4b5k

Go back to Iron Binding Sites List in 4b5k
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:15.4
occ:1.00
 FE B:HDD900 0.0 15.4 1.0
OH B:TYR369 2.0 13.7 1.0
ND B:HDD900 2.0 14.5 1.0
NC B:HDD900 2.1 15.5 1.0
NA B:HDD900 2.1 14.8 1.0
NB B:HDD900 2.1 15.6 1.0
O B:HOH2094 2.5 21.3 0.3
CZ B:TYR369 3.0 12.5 1.0
C1D B:HDD900 3.0 14.5 1.0
C4D B:HDD900 3.0 14.9 1.0
C4C B:HDD900 3.0 14.3 1.0
C4A B:HDD900 3.1 15.3 1.0
C1A B:HDD900 3.1 14.5 1.0
C4B B:HDD900 3.1 15.2 1.0
C1B B:HDD900 3.1 15.6 1.0
C1C B:HDD900 3.1 14.7 1.0
CHD B:HDD900 3.4 14.3 1.0
CHA B:HDD900 3.4 14.6 1.0
CHB B:HDD900 3.4 15.2 1.0
CHC B:HDD900 3.5 14.5 1.0
CE1 B:TYR369 3.8 12.4 1.0
CE2 B:TYR369 3.8 12.3 1.0
NE B:ARG365 4.1 14.2 1.0
NH2 B:ARG365 4.2 13.2 1.0
O B:HOH2095 4.3 28.0 1.0
C3C B:HDD900 4.3 14.3 1.0
C3B B:HDD900 4.4 15.5 1.0
C3D B:HDD900 4.4 15.4 1.0
C3A B:HDD900 4.4 13.6 1.0
C2A B:HDD900 4.4 13.9 1.0
C2D B:HDD900 4.4 15.4 1.0
C2C B:HDD900 4.4 14.7 1.0
C2B B:HDD900 4.4 15.9 1.0
CG2 B:VAL81 4.5 13.3 1.0
CZ B:ARG365 4.6 14.9 1.0
CZ B:PHE168 4.7 15.2 1.0
CD2 B:HIS82 4.8 14.9 1.0
NE2 B:HIS82 4.8 15.5 1.0

Iron binding site 3 out of 4 in 4b5k

Go back to Iron Binding Sites List in 4b5k
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:13.8
occ:1.00
 FE C:HDD900 0.0 13.8 1.0
OH C:TYR369 2.0 12.9 1.0
ND C:HDD900 2.0 13.1 1.0
NA C:HDD900 2.1 12.1 1.0
NC C:HDD900 2.1 13.4 1.0
NB C:HDD900 2.1 14.3 1.0
O C:HOH2032 2.5 15.1 0.3
CZ C:TYR369 3.0 11.2 1.0
C1D C:HDD900 3.0 13.8 1.0
C4D C:HDD900 3.0 13.2 1.0
C4A C:HDD900 3.0 13.2 1.0
C4C C:HDD900 3.1 14.2 1.0
C1A C:HDD900 3.1 12.5 1.0
C1C C:HDD900 3.1 14.2 1.0
C4B C:HDD900 3.1 14.7 1.0
C1B C:HDD900 3.1 13.6 1.0
CHD C:HDD900 3.4 12.8 1.0
CHA C:HDD900 3.4 12.5 1.0
CHB C:HDD900 3.5 12.9 1.0
CHC C:HDD900 3.5 14.3 1.0
CE1 C:TYR369 3.7 11.2 1.0
CE2 C:TYR369 3.7 11.5 1.0
NE C:ARG365 4.1 11.3 1.0
NH2 C:ARG365 4.2 11.1 1.0
O C:HOH2031 4.2 22.7 1.0
C3A C:HDD900 4.3 12.5 1.0
C3C C:HDD900 4.3 13.9 1.0
C2A C:HDD900 4.3 11.9 1.0
C3D C:HDD900 4.4 13.9 1.0
C2C C:HDD900 4.4 13.8 1.0
C2D C:HDD900 4.4 13.2 1.0
C3B C:HDD900 4.4 14.7 1.0
C2B C:HDD900 4.4 14.4 1.0
CG2 C:VAL81 4.5 11.9 1.0
CZ C:PHE168 4.6 14.6 1.0
CZ C:ARG365 4.6 11.6 1.0
CD2 C:HIS82 4.8 11.8 1.0
NE2 C:HIS82 4.9 12.6 1.0
CE2 C:PHE168 4.9 14.2 1.0
CD1 C:TYR369 5.0 11.5 1.0
CD2 C:TYR369 5.0 11.4 1.0

Iron binding site 4 out of 4 in 4b5k

Go back to Iron Binding Sites List in 4b5k
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:14.3
occ:1.00
 FE D:HDD900 0.0 14.3 1.0
ND D:HDD900 2.0 13.7 1.0
OH D:TYR369 2.0 15.3 1.0
NA D:HDD900 2.1 13.8 1.0
NC D:HDD900 2.1 13.1 1.0
NB D:HDD900 2.1 15.4 1.0
O D:HOH2030 2.4 19.0 0.3
CZ D:TYR369 3.0 12.9 1.0
C4D D:HDD900 3.0 14.3 1.0
C1D D:HDD900 3.0 14.4 1.0
C4C D:HDD900 3.1 13.4 1.0
C1A D:HDD900 3.1 13.6 1.0
C1B D:HDD900 3.1 14.4 1.0
C4A D:HDD900 3.1 13.8 1.0
C4B D:HDD900 3.1 15.1 1.0
C1C D:HDD900 3.1 14.1 1.0
CHA D:HDD900 3.4 13.9 1.0
CHD D:HDD900 3.5 13.6 1.0
CHB D:HDD900 3.5 13.9 1.0
CHC D:HDD900 3.5 13.8 1.0
CE2 D:TYR369 3.7 12.7 1.0
CE1 D:TYR369 3.8 12.8 1.0
NE D:ARG365 4.2 12.6 1.0
NH2 D:ARG365 4.2 11.9 1.0
O D:HOH2031 4.3 26.8 1.0
C3C D:HDD900 4.3 13.9 1.0
C3B D:HDD900 4.4 15.6 1.0
C3A D:HDD900 4.4 13.3 1.0
C3D D:HDD900 4.4 14.9 1.0
C2A D:HDD900 4.4 13.3 1.0
C2D D:HDD900 4.4 15.0 1.0
C2C D:HDD900 4.4 13.1 1.0
C2B D:HDD900 4.4 15.1 1.0
CG2 D:VAL81 4.5 13.9 1.0
CZ D:PHE168 4.6 16.9 1.0
CZ D:ARG365 4.6 12.8 1.0
CD2 D:HIS82 4.8 14.4 1.0
NE2 D:HIS82 4.8 14.9 1.0
CE2 D:PHE168 5.0 16.8 1.0
CD2 D:TYR369 5.0 12.0 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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