Atomistry » Iron » PDB 4a9v-4b2y » 4b2y
Atomistry »
  Iron »
    PDB 4a9v-4b2y »
      4b2y »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy