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Iron in PDB 4b2y: 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: 4b2y 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) 29.01 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.323, 121.205, 124.965, 90.00, 115.54, 90.00
R / Rfree (%) 15 / 18.1

Other elements in 4b2y:

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

Calcium (Ca) 6 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 4b2y). 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: 4b2y:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4b2y

Go back to Iron Binding Sites List in 4b2y
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:Fe754

b:13.0
occ:1.00
 FE A:HEM754 0.0 13.0 1.0
OH A:TYR369 1.9 12.5 1.0
NA A:HEM754 2.0 12.1 1.0
NC A:HEM754 2.0 12.5 1.0
ND A:HEM754 2.1 12.7 1.0
NB A:HEM754 2.1 12.6 1.0
CZ A:TYR369 2.9 12.9 1.0
O A:HOH2107 2.9 16.6 0.3
C4C A:HEM754 3.0 12.6 1.0
C4A A:HEM754 3.0 12.2 1.0
C1D A:HEM754 3.1 13.0 1.0
C1A A:HEM754 3.1 12.1 1.0
C1C A:HEM754 3.1 12.3 1.0
C4B A:HEM754 3.1 12.5 1.0
C4D A:HEM754 3.1 12.5 1.0
C1B A:HEM754 3.2 12.7 1.0
CHD A:HEM754 3.4 12.5 1.0
CHB A:HEM754 3.5 12.0 1.0
CHC A:HEM754 3.5 11.9 1.0
CHA A:HEM754 3.5 12.1 1.0
CE2 A:TYR369 3.6 12.7 1.0
CE1 A:TYR369 3.8 12.7 1.0
NE A:ARG365 4.0 12.0 1.0
NH2 A:ARG365 4.1 11.2 1.0
C3C A:HEM754 4.3 12.8 1.0
C3A A:HEM754 4.3 11.6 1.0
C2C A:HEM754 4.4 12.3 1.0
C2A A:HEM754 4.4 11.9 1.0
C3B A:HEM754 4.4 12.6 1.0
C2D A:HEM754 4.4 13.0 1.0
C3D A:HEM754 4.4 13.2 1.0
CG2 A:VAL81 4.5 10.6 1.0
C2B A:HEM754 4.5 12.5 1.0
CZ A:ARG365 4.5 12.4 1.0
O A:HOH2106 4.7 24.6 1.0
CZ A:PHE168 4.7 11.4 1.0
CD2 A:HIS82 4.8 11.1 1.0
CD2 A:TYR369 4.9 12.7 1.0
NE2 A:HIS82 5.0 12.6 1.0

Iron binding site 2 out of 4 in 4b2y

Go back to Iron Binding Sites List in 4b2y
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:Fe754

b:13.1
occ:1.00
 FE B:HEM754 0.0 13.1 1.0
OH B:TYR369 1.9 11.9 1.0
NC B:HEM754 2.0 13.2 1.0
NA B:HEM754 2.0 12.4 1.0
ND B:HEM754 2.1 13.0 1.0
NB B:HEM754 2.1 13.7 1.0
O B:HOH2101 2.8 16.7 0.3
CZ B:TYR369 2.9 11.7 1.0
C4C B:HEM754 3.0 12.9 1.0
C4A B:HEM754 3.1 12.4 1.0
C1C B:HEM754 3.1 13.0 1.0
C1A B:HEM754 3.1 12.4 1.0
C1D B:HEM754 3.1 13.2 1.0
C4B B:HEM754 3.1 14.0 1.0
C4D B:HEM754 3.1 13.2 1.0
C1B B:HEM754 3.1 13.9 1.0
CHD B:HEM754 3.5 12.9 1.0
CHB B:HEM754 3.5 12.9 1.0
CHA B:HEM754 3.5 12.7 1.0
CHC B:HEM754 3.5 13.0 1.0
CE2 B:TYR369 3.6 11.7 1.0
CE1 B:TYR369 3.8 12.1 1.0
NE B:ARG365 4.0 12.3 1.0
NH2 B:ARG365 4.1 11.5 1.0
C3C B:HEM754 4.3 12.9 1.0
C2C B:HEM754 4.4 12.6 1.0
C2A B:HEM754 4.4 11.8 1.0
C3A B:HEM754 4.4 12.1 1.0
C3B B:HEM754 4.4 13.9 1.0
C3D B:HEM754 4.4 13.3 1.0
C2D B:HEM754 4.4 13.6 1.0
C2B B:HEM754 4.4 13.7 1.0
CZ B:ARG365 4.5 12.7 1.0
CG2 B:VAL81 4.5 9.3 1.0
O B:HOH2100 4.7 25.1 1.0
CZ B:PHE168 4.7 11.0 1.0
CD2 B:TYR369 4.9 11.2 1.0
CD2 B:HIS82 4.9 11.3 1.0
CD1 B:TYR369 5.0 11.4 1.0

Iron binding site 3 out of 4 in 4b2y

Go back to Iron Binding Sites List in 4b2y
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:Fe754

b:13.3
occ:1.00
 FE C:HEM754 0.0 13.3 1.0
OH C:TYR369 1.9 12.3 1.0
NA C:HEM754 2.0 11.7 1.0
NC C:HEM754 2.0 12.8 1.0
ND C:HEM754 2.1 12.7 1.0
NB C:HEM754 2.1 12.9 1.0
O C:HOH2038 2.7 13.7 0.3
CZ C:TYR369 2.9 12.4 1.0
C4C C:HEM754 3.0 12.5 1.0
C1A C:HEM754 3.1 11.6 1.0
C1C C:HEM754 3.1 12.3 1.0
C1D C:HEM754 3.1 12.6 1.0
C4D C:HEM754 3.1 12.7 1.0
C4B C:HEM754 3.1 13.2 1.0
C4A C:HEM754 3.1 11.5 1.0
C1B C:HEM754 3.1 13.0 1.0
CHD C:HEM754 3.5 12.5 1.0
CHA C:HEM754 3.5 11.7 1.0
CHC C:HEM754 3.5 12.7 1.0
CHB C:HEM754 3.5 11.9 1.0
CE2 C:TYR369 3.6 12.5 1.0
CE1 C:TYR369 3.8 11.8 1.0
NE C:ARG365 4.1 10.6 1.0
NH2 C:ARG365 4.2 10.2 1.0
C3C C:HEM754 4.3 13.0 1.0
C2A C:HEM754 4.4 11.0 1.0
C2C C:HEM754 4.4 12.6 1.0
C3A C:HEM754 4.4 11.1 1.0
C3B C:HEM754 4.4 13.1 1.0
C3D C:HEM754 4.4 12.9 1.0
C2D C:HEM754 4.4 12.9 1.0
C2B C:HEM754 4.5 12.8 1.0
CG2 C:VAL81 4.5 10.0 1.0
CZ C:ARG365 4.5 10.5 1.0
CZ C:PHE168 4.7 13.3 1.0
O C:HOH2037 4.9 23.1 1.0
CD2 C:TYR369 4.9 12.7 1.0
CD2 C:HIS82 4.9 11.7 1.0

Iron binding site 4 out of 4 in 4b2y

Go back to Iron Binding Sites List in 4b2y
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:Fe754

b:13.2
occ:1.00
 FE D:HEM754 0.0 13.2 1.0
OH D:TYR369 2.0 12.1 1.0
NA D:HEM754 2.0 12.3 1.0
NC D:HEM754 2.0 12.6 1.0
ND D:HEM754 2.1 12.5 1.0
NB D:HEM754 2.1 13.4 1.0
O D:HOH2033 2.9 18.1 0.3
CZ D:TYR369 2.9 12.1 1.0
C4A D:HEM754 3.1 11.8 1.0
C4C D:HEM754 3.1 12.6 1.0
C1A D:HEM754 3.1 12.0 1.0
C4B D:HEM754 3.1 13.4 1.0
C1D D:HEM754 3.1 12.0 1.0
C1C D:HEM754 3.1 12.7 1.0
C4D D:HEM754 3.1 12.3 1.0
C1B D:HEM754 3.1 13.0 1.0
CHD D:HEM754 3.5 12.2 1.0
CHB D:HEM754 3.5 12.2 1.0
CHC D:HEM754 3.5 12.6 1.0
CHA D:HEM754 3.5 11.8 1.0
CE2 D:TYR369 3.6 11.6 1.0
CE1 D:TYR369 3.8 11.6 1.0
NE D:ARG365 4.1 10.1 1.0
NH2 D:ARG365 4.2 10.1 1.0
C3A D:HEM754 4.3 11.7 1.0
C3C D:HEM754 4.3 12.9 1.0
C2A D:HEM754 4.4 11.8 1.0
C3B D:HEM754 4.4 13.7 1.0
C2C D:HEM754 4.4 12.9 1.0
C2D D:HEM754 4.4 12.2 1.0
C3D D:HEM754 4.4 12.4 1.0
CG2 D:VAL81 4.4 10.4 1.0
C2B D:HEM754 4.5 13.2 1.0
CZ D:ARG365 4.5 10.5 1.0
CZ D:PHE168 4.7 13.4 1.0
CD2 D:TYR369 4.8 11.4 1.0
CD2 D:HIS82 4.9 12.6 1.0
O D:HOH2034 4.9 32.2 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: ESSN 1744-3091
PubMed: 23545640
DOI: 10.1107/S1744309113004211
Page generated: Sun Aug 4 23:50:22 2024

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