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Iron in PDB 5zz1: 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: 5zz1 was solved by Y.Yuzugullu Karakus, 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) 29.40 / 1.91
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.528, 121.677, 185.454, 90.00, 102.16, 90.00
R / Rfree (%) 14.2 / 17.4

Other elements in 5zz1:

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 5zz1). 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: 5zz1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5zz1

Go back to Iron Binding Sites List in 5zz1
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:Fe701

b:12.3
occ:1.00
 FE A:HDD701 0.0 12.3 1.0
OH A:TYR369 1.9 10.8 1.0
ND A:HDD701 2.0 12.1 1.0
NA A:HDD701 2.0 11.6 1.0
NB A:HDD701 2.1 12.4 1.0
NC A:HDD701 2.1 11.9 1.0
O A:HOH937 2.5 51.0 1.0
CZ A:TYR369 2.9 11.4 1.0
C4A A:HDD701 3.0 11.4 1.0
C4D A:HDD701 3.0 12.2 1.0
C1A A:HDD701 3.1 11.0 1.0
C1D A:HDD701 3.1 12.6 1.0
C4C A:HDD701 3.1 12.1 1.0
C1C A:HDD701 3.1 12.1 1.0
C4B A:HDD701 3.1 12.7 1.0
C1B A:HDD701 3.1 12.3 1.0
CHA A:HDD701 3.4 11.6 1.0
CHB A:HDD701 3.4 11.8 1.0
CHC A:HDD701 3.4 12.2 1.0
CHD A:HDD701 3.4 11.5 1.0
CE2 A:TYR369 3.7 11.6 1.0
CE1 A:TYR369 3.8 11.6 1.0
NE A:ARG365 4.1 10.9 1.0
NH2 A:ARG365 4.2 9.9 1.0
C3A A:HDD701 4.3 11.2 1.0
C2A A:HDD701 4.3 10.7 1.0
C3C A:HDD701 4.3 12.5 1.0
C3B A:HDD701 4.3 12.6 1.0
C2B A:HDD701 4.4 12.4 1.0
C3D A:HDD701 4.4 14.2 1.0
C2C A:HDD701 4.4 12.3 1.0
C2D A:HDD701 4.4 13.6 1.0
O A:HOH929 4.5 25.1 1.0
CZ A:ARG365 4.6 10.5 1.0
CG2 A:VAL81 4.6 10.0 1.0
CZ A:PHE168 4.7 13.3 1.0
NE2 A:HIS82 4.8 10.8 1.0
CD2 A:HIS82 4.8 10.7 1.0
CD2 A:TYR369 4.9 12.0 1.0
CD1 A:TYR369 5.0 11.8 1.0

Iron binding site 2 out of 4 in 5zz1

Go back to Iron Binding Sites List in 5zz1
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:Fe1702

b:12.5
occ:1.00
 FE B:HDD1702 0.0 12.5 1.0
OH B:TYR369 1.9 11.2 1.0
ND B:HDD1702 2.0 12.6 1.0
NC B:HDD1702 2.1 12.5 1.0
NB B:HDD1702 2.1 12.5 1.0
NA B:HDD1702 2.1 12.4 1.0
CZ B:TYR369 3.0 11.3 1.0
C4C B:HDD1702 3.0 12.3 1.0
C1D B:HDD1702 3.1 13.1 1.0
C4A B:HDD1702 3.1 11.6 1.0
C1A B:HDD1702 3.1 11.5 1.0
C4D B:HDD1702 3.1 12.9 1.0
C1C B:HDD1702 3.1 12.3 1.0
C4B B:HDD1702 3.1 12.6 1.0
C1B B:HDD1702 3.1 12.5 1.0
CHD B:HDD1702 3.4 12.1 1.0
CHA B:HDD1702 3.4 11.9 1.0
CHB B:HDD1702 3.4 11.9 1.0
CHC B:HDD1702 3.5 12.5 1.0
O B:HOH2174 3.6 56.8 1.0
CE2 B:TYR369 3.7 11.2 1.0
CE1 B:TYR369 3.8 11.0 1.0
NE B:ARG365 4.1 12.1 1.0
NH2 B:ARG365 4.2 10.8 1.0
C3A B:HDD1702 4.3 11.6 1.0
C2A B:HDD1702 4.3 11.3 1.0
C3B B:HDD1702 4.3 12.6 1.0
C3C B:HDD1702 4.3 12.6 1.0
C2D B:HDD1702 4.4 13.8 1.0
C2C B:HDD1702 4.4 12.8 1.0
C3D B:HDD1702 4.4 14.2 1.0
C2B B:HDD1702 4.4 12.5 1.0
CG2 B:VAL81 4.6 11.6 1.0
O B:HOH2053 4.6 22.1 1.0
CZ B:ARG365 4.6 11.9 1.0
CZ B:PHE168 4.7 13.5 1.0
CD2 B:HIS82 4.8 10.9 1.0
NE2 B:HIS82 4.8 11.4 1.0
CD2 B:TYR369 4.9 10.8 1.0

Iron binding site 3 out of 4 in 5zz1

Go back to Iron Binding Sites List in 5zz1
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:Fe701

b:12.7
occ:1.00
 FE C:HDD701 0.0 12.7 1.0
OH C:TYR369 1.9 10.8 1.0
ND C:HDD701 2.0 11.9 1.0
NA C:HDD701 2.0 11.0 1.0
NB C:HDD701 2.1 11.8 1.0
NC C:HDD701 2.1 12.0 1.0
O C:HOH1185 2.8 37.7 1.0
CZ C:TYR369 3.0 10.9 1.0
C4A C:HDD701 3.0 10.7 1.0
C4D C:HDD701 3.0 12.1 1.0
C1A C:HDD701 3.0 10.9 1.0
C1D C:HDD701 3.0 12.5 1.0
C4B C:HDD701 3.1 12.3 1.0
C4C C:HDD701 3.1 12.1 1.0
C1C C:HDD701 3.1 12.2 1.0
C1B C:HDD701 3.1 11.6 1.0
CHA C:HDD701 3.4 10.8 1.0
CHD C:HDD701 3.4 11.9 1.0
CHC C:HDD701 3.4 12.3 1.0
CHB C:HDD701 3.4 10.9 1.0
CE2 C:TYR369 3.7 11.0 1.0
CE1 C:TYR369 3.8 11.1 1.0
NE C:ARG365 4.1 11.8 1.0
NH2 C:ARG365 4.2 11.0 1.0
C3A C:HDD701 4.3 10.2 1.0
C2A C:HDD701 4.3 10.2 1.0
C3C C:HDD701 4.3 12.5 1.0
C3B C:HDD701 4.3 12.4 1.0
C3D C:HDD701 4.4 13.4 1.0
C2D C:HDD701 4.4 13.4 1.0
C2C C:HDD701 4.4 12.8 1.0
O C:HOH959 4.4 24.6 1.0
C2B C:HDD701 4.4 11.8 1.0
CZ C:ARG365 4.6 11.4 1.0
CG2 C:VAL81 4.6 10.5 1.0
CZ C:PHE168 4.7 12.8 1.0
CD2 C:HIS82 4.8 10.8 1.0
NE2 C:HIS82 4.8 11.3 1.0
CD2 C:TYR369 5.0 10.7 1.0
O1D C:HDD701 5.0 15.9 1.0

Iron binding site 4 out of 4 in 5zz1

Go back to Iron Binding Sites List in 5zz1
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:Fe701

b:13.4
occ:1.00
 FE D:HDD701 0.0 13.4 1.0
OH D:TYR369 1.9 12.9 1.0
ND D:HDD701 2.0 13.3 1.0
NA D:HDD701 2.0 12.4 1.0
NC D:HDD701 2.1 13.4 1.0
NB D:HDD701 2.1 13.3 1.0
O D:HOH1145 2.6 42.7 1.0
CZ D:TYR369 2.9 12.4 1.0
C4A D:HDD701 3.0 12.7 1.0
C1D D:HDD701 3.0 13.2 1.0
C4D D:HDD701 3.0 13.4 1.0
C1A D:HDD701 3.0 12.1 1.0
C4C D:HDD701 3.0 13.3 1.0
C4B D:HDD701 3.1 13.5 1.0
C1B D:HDD701 3.1 13.5 1.0
C1C D:HDD701 3.1 13.1 1.0
CHB D:HDD701 3.4 12.9 1.0
CHA D:HDD701 3.4 12.1 1.0
CHD D:HDD701 3.4 12.9 1.0
CHC D:HDD701 3.4 13.2 1.0
CE2 D:TYR369 3.7 11.9 1.0
CE1 D:TYR369 3.7 12.3 1.0
NE D:ARG365 4.1 12.6 1.0
NH2 D:ARG365 4.2 11.8 1.0
C3C D:HDD701 4.3 13.3 1.0
C2A D:HDD701 4.3 12.0 1.0
C3A D:HDD701 4.3 12.1 1.0
C3B D:HDD701 4.3 13.4 1.0
O D:HOH1045 4.3 26.0 1.0
C2B D:HDD701 4.4 13.5 1.0
C2C D:HDD701 4.4 13.0 1.0
C3D D:HDD701 4.4 14.4 1.0
C2D D:HDD701 4.4 13.9 1.0
CG2 D:VAL81 4.5 11.1 1.0
CZ D:ARG365 4.6 12.2 1.0
CZ D:PHE168 4.7 14.0 1.0
CD2 D:HIS82 4.8 11.0 1.0
NE2 D:HIS82 4.8 11.1 1.0
CD2 D:TYR369 5.0 11.8 1.0
CD1 D:TYR369 5.0 12.3 1.0

Reference:

Y.Yuzugullu Karakus, G.Goc, S.Balci, B.A.Yorke, C.H.Trinh, M.J.Mcpherson, A.R.Pearson. Identification of the Site of Oxidase Substrate Binding in Scytalidium Thermophilum Catalase. Acta Crystallogr D Struct V. 74 979 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30289408
DOI: 10.1107/S2059798318010628
Page generated: Tue Aug 6 13:22:28 2024

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