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Iron in PDB 6rjr: Crystal Structure of A Fungal Catalase at 1.9 Angstrom

Enzymatic activity of Crystal Structure of A Fungal Catalase at 1.9 Angstrom

All present enzymatic activity of Crystal Structure of A Fungal Catalase at 1.9 Angstrom:
1.11.1.6;

Protein crystallography data

The structure of Crystal Structure of A Fungal Catalase at 1.9 Angstrom, PDB code: 6rjr was solved by S.Gomez, S.Navas-Yuste, A.M.Payne, W.Rivera, M.Lopez-Estepa, C.Brangbour, D.Fulla, J.Juanhuix, F.J.Fernandez, M.C.Vega, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.98 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.670, 131.620, 176.670, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 24.1

Other elements in 6rjr:

The structure of Crystal Structure of A Fungal Catalase at 1.9 Angstrom also contains other interesting chemical elements:

Potassium (K) 4 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom (pdb code 6rjr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom, PDB code: 6rjr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6rjr

Go back to Iron Binding Sites List in 6rjr
Iron binding site 1 out of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:21.2
occ:1.00
FE A:HEM601 0.0 21.2 1.0
OH A:TYR349 1.8 29.0 1.0
ND A:HEM601 2.0 17.6 1.0
NC A:HEM601 2.1 16.1 1.0
NB A:HEM601 2.1 11.5 1.0
NA A:HEM601 2.1 19.5 1.0
CZ A:TYR349 2.9 13.2 1.0
C1D A:HEM601 2.9 11.2 1.0
C4C A:HEM601 2.9 10.6 1.0
C4A A:HEM601 3.0 10.1 1.0
C1B A:HEM601 3.1 14.1 1.0
C4D A:HEM601 3.1 15.2 1.0
C1C A:HEM601 3.1 10.7 1.0
C1A A:HEM601 3.1 12.7 1.0
C4B A:HEM601 3.2 11.9 1.0
CHD A:HEM601 3.2 19.0 1.0
CHB A:HEM601 3.4 10.2 1.0
CHA A:HEM601 3.5 25.4 1.0
CHC A:HEM601 3.5 14.6 1.0
CE2 A:TYR349 3.6 13.2 1.0
CE1 A:TYR349 3.7 18.4 1.0
NE A:ARG345 4.0 13.6 1.0
NH2 A:ARG345 4.0 18.3 1.0
C2D A:HEM601 4.1 17.0 1.0
C3C A:HEM601 4.2 14.0 1.0
C3D A:HEM601 4.2 10.7 1.0
C3A A:HEM601 4.2 15.9 1.0
C2C A:HEM601 4.3 11.1 1.0
C2B A:HEM601 4.3 10.6 1.0
C2A A:HEM601 4.3 10.6 1.0
O A:HOH764 4.3 16.9 1.0
C3B A:HEM601 4.3 18.5 1.0
CZ A:ARG345 4.4 16.6 1.0
CZ A:PHE150 4.6 16.1 1.0
CD2 A:HIS64 4.7 12.9 1.0
NE2 A:HIS64 4.7 16.8 1.0
CD2 A:TYR349 4.9 21.6 1.0
CD1 A:TYR349 5.0 25.6 1.0
CD A:ARG345 5.0 16.5 1.0

Iron binding site 2 out of 4 in 6rjr

Go back to Iron Binding Sites List in 6rjr
Iron binding site 2 out of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:28.2
occ:1.00
FE B:HEM601 0.0 28.2 1.0
NB B:HEM601 2.0 27.6 1.0
ND B:HEM601 2.0 17.9 1.0
NC B:HEM601 2.0 31.1 1.0
OH B:TYR349 2.0 25.8 1.0
NA B:HEM601 2.1 18.6 1.0
C1D B:HEM601 2.9 17.9 1.0
C4C B:HEM601 3.0 17.8 1.0
C1B B:HEM601 3.0 22.6 1.0
CZ B:TYR349 3.0 21.5 1.0
C4B B:HEM601 3.0 22.3 1.0
C4A B:HEM601 3.1 19.3 1.0
C1C B:HEM601 3.1 22.7 1.0
C4D B:HEM601 3.1 27.1 1.0
C1A B:HEM601 3.2 18.9 1.0
CHD B:HEM601 3.3 26.6 1.0
CHB B:HEM601 3.4 19.5 1.0
CHC B:HEM601 3.4 30.4 1.0
CHA B:HEM601 3.5 18.6 1.0
CE1 B:TYR349 3.8 21.4 1.0
CE2 B:TYR349 3.8 21.2 1.0
NE B:ARG345 4.0 23.4 1.0
NH2 B:ARG345 4.0 23.2 1.0
O B:HOH798 4.1 21.9 1.0
C3C B:HEM601 4.2 19.3 1.0
C2D B:HEM601 4.2 18.2 1.0
C2B B:HEM601 4.2 19.6 1.0
C2C B:HEM601 4.2 19.1 1.0
C3B B:HEM601 4.2 19.1 1.0
C3D B:HEM601 4.3 18.3 1.0
C3A B:HEM601 4.3 29.4 1.0
C2A B:HEM601 4.4 19.7 1.0
CZ B:ARG345 4.4 24.0 1.0
CZ B:PHE150 4.6 22.6 1.0
NE2 B:HIS64 4.7 22.0 1.0
CD2 B:HIS64 4.7 34.0 1.0
CD B:ARG345 5.0 23.0 1.0

Iron binding site 3 out of 4 in 6rjr

Go back to Iron Binding Sites List in 6rjr
Iron binding site 3 out of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe601

b:22.5
occ:1.00
FE C:HEM601 0.0 22.5 1.0
OH C:TYR349 1.7 17.5 1.0
NA C:HEM601 1.9 12.2 1.0
NC C:HEM601 2.1 12.1 1.0
ND C:HEM601 2.1 14.2 1.0
NB C:HEM601 2.1 19.2 1.0
CZ C:TYR349 2.7 27.9 1.0
C4A C:HEM601 2.9 27.4 1.0
C1A C:HEM601 3.0 14.3 1.0
C4C C:HEM601 3.0 17.8 1.0
C4D C:HEM601 3.1 10.8 1.0
C1B C:HEM601 3.1 30.6 1.0
C1D C:HEM601 3.1 17.2 1.0
C1C C:HEM601 3.1 13.5 1.0
C4B C:HEM601 3.1 14.5 1.0
CHB C:HEM601 3.4 20.6 1.0
CHA C:HEM601 3.4 14.6 1.0
CHD C:HEM601 3.4 12.2 1.0
CHC C:HEM601 3.5 13.2 1.0
CE2 C:TYR349 3.5 12.1 1.0
CE1 C:TYR349 3.6 22.6 1.0
NE C:ARG345 4.0 23.8 1.0
NH2 C:ARG345 4.1 20.4 1.0
C3A C:HEM601 4.1 13.8 1.0
C2A C:HEM601 4.2 11.2 1.0
O C:HOH775 4.2 16.6 1.0
C3C C:HEM601 4.2 13.0 1.0
C2B C:HEM601 4.3 17.8 1.0
C3D C:HEM601 4.3 24.9 1.0
C2C C:HEM601 4.3 13.0 1.0
C2D C:HEM601 4.3 22.5 1.0
C3B C:HEM601 4.3 20.5 1.0
CZ C:ARG345 4.4 23.4 1.0
CZ C:PHE150 4.6 13.2 1.0
CD2 C:HIS64 4.7 27.4 1.0
NE2 C:HIS64 4.7 14.3 1.0
CD2 C:TYR349 4.8 24.8 1.0
CD1 C:TYR349 4.9 24.2 1.0
CD C:ARG345 5.0 17.7 1.0

Iron binding site 4 out of 4 in 6rjr

Go back to Iron Binding Sites List in 6rjr
Iron binding site 4 out of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe602

b:16.5
occ:1.00
FE D:HEM602 0.0 16.5 1.0
OH D:TYR349 1.8 15.3 1.0
NC D:HEM602 2.0 26.6 1.0
ND D:HEM602 2.0 18.1 1.0
NA D:HEM602 2.1 16.4 1.0
NB D:HEM602 2.1 32.7 1.0
CZ D:TYR349 2.8 12.3 1.0
C4C D:HEM602 3.0 20.5 1.0
C1D D:HEM602 3.0 18.6 1.0
C1C D:HEM602 3.0 16.5 1.0
C4A D:HEM602 3.1 16.2 1.0
C4B D:HEM602 3.1 20.2 1.0
C1B D:HEM602 3.1 16.1 1.0
C4D D:HEM602 3.1 16.9 1.0
C1A D:HEM602 3.1 19.0 1.0
CHD D:HEM602 3.4 17.0 1.0
CHC D:HEM602 3.4 22.4 1.0
CHB D:HEM602 3.4 16.1 1.0
CHA D:HEM602 3.5 31.9 1.0
CE2 D:TYR349 3.6 20.5 1.0
CE1 D:TYR349 3.7 28.7 1.0
NE D:ARG345 4.1 17.6 1.0
NH2 D:ARG345 4.1 27.2 1.0
O D:HOH748 4.2 23.8 1.0
C3C D:HEM602 4.2 23.4 1.0
C2C D:HEM602 4.2 16.7 1.0
C3B D:HEM602 4.3 20.9 1.0
C2D D:HEM602 4.3 26.6 1.0
C2B D:HEM602 4.3 25.2 1.0
C3D D:HEM602 4.3 19.7 1.0
C3A D:HEM602 4.3 22.7 1.0
C2A D:HEM602 4.3 18.3 1.0
CZ D:ARG345 4.5 20.3 1.0
CZ D:PHE150 4.6 13.3 1.0
CD2 D:HIS64 4.8 24.5 1.0
NE2 D:HIS64 4.8 26.0 1.0
CD1 D:TYR349 4.9 22.5 1.0
CD2 D:TYR349 4.9 19.8 1.0

Reference:

S.Gomez, S.Navas-Yuste, A.M.Payne, W.Rivera, M.Lopez-Estepa, C.Brangbour, D.Fulla, J.Juanhuix, F.J.Fernandez, M.C.Vega. Peroxisomal Catalases From the Yeasts Pichia Pastoris and Kluyveromyces Lactis As Models For Oxidative Damage in Higher Eukaryotes. Free Radic. Biol. Med. V. 141 279 2019.
ISSN: ISSN 1873-4596
PubMed: 31238127
DOI: 10.1016/J.FREERADBIOMED.2019.06.025
Page generated: Wed Aug 7 08:45:13 2024

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