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Iron in PDB 6rjn: Crystal Structure of A Fungal Catalase at 2.3 Angstroms

Enzymatic activity of Crystal Structure of A Fungal Catalase at 2.3 Angstroms

All present enzymatic activity of Crystal Structure of A Fungal Catalase at 2.3 Angstroms:
1.11.1.6;

Protein crystallography data

The structure of Crystal Structure of A Fungal Catalase at 2.3 Angstroms, PDB code: 6rjn 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) 54.67 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 165.943, 173.690, 96.490, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 19.6

Other elements in 6rjn:

The structure of Crystal Structure of A Fungal Catalase at 2.3 Angstroms also contains other interesting chemical elements:

Potassium (K) 7 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms (pdb code 6rjn). 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 2.3 Angstroms, PDB code: 6rjn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6rjn

Go back to Iron Binding Sites List in 6rjn
Iron binding site 1 out of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


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 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:28.9
occ:1.00
FE A:HEM601 0.0 28.9 1.0
ND A:HEM601 1.9 26.8 1.0
NA A:HEM601 2.0 24.6 1.0
NC A:HEM601 2.1 32.5 1.0
NB A:HEM601 2.1 28.6 1.0
OH A:TYR349 2.2 19.6 1.0
C1D A:HEM601 2.9 23.9 1.0
C4D A:HEM601 2.9 21.3 1.0
C1A A:HEM601 2.9 23.4 1.0
C4C A:HEM601 3.0 28.1 1.0
C4A A:HEM601 3.0 23.1 1.0
C4B A:HEM601 3.1 25.6 1.0
C1B A:HEM601 3.1 23.3 1.0
C1C A:HEM601 3.1 20.3 1.0
CZ A:TYR349 3.1 20.5 1.0
CHD A:HEM601 3.3 20.9 1.0
CHA A:HEM601 3.3 20.0 1.0
CHB A:HEM601 3.4 20.9 1.0
CHC A:HEM601 3.5 26.5 1.0
CE2 A:TYR349 3.8 19.0 1.0
CE1 A:TYR349 3.9 25.8 1.0
C2D A:HEM601 4.1 20.8 1.0
C2A A:HEM601 4.1 22.4 1.0
C3D A:HEM601 4.1 23.1 1.0
NE A:ARG345 4.2 18.9 1.0
C3A A:HEM601 4.2 22.8 1.0
C3C A:HEM601 4.2 27.3 1.0
C2C A:HEM601 4.2 30.5 1.0
C2B A:HEM601 4.3 24.4 1.0
C3B A:HEM601 4.3 24.2 1.0
O A:HOH865 4.4 28.6 1.0
NH2 A:ARG345 4.4 24.0 1.0
CZ A:PHE152 4.6 24.5 1.0
CG2 A:VAL65 4.6 22.9 1.0
CD2 A:HIS66 4.7 22.3 1.0
NE2 A:HIS66 4.7 19.5 1.0
CZ A:ARG345 4.7 23.1 1.0

Iron binding site 2 out of 4 in 6rjn

Go back to Iron Binding Sites List in 6rjn
Iron binding site 2 out of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


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 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:30.8
occ:1.00
FE B:HEM602 0.0 30.8 1.0
OH B:TYR349 1.9 18.0 1.0
ND B:HEM602 2.0 22.4 1.0
NB B:HEM602 2.0 22.9 1.0
NA B:HEM602 2.1 17.2 1.0
NC B:HEM602 2.1 28.2 1.0
CZ B:TYR349 2.9 18.3 1.0
C4D B:HEM602 3.0 24.7 1.0
C4B B:HEM602 3.0 24.4 1.0
C1C B:HEM602 3.1 25.9 1.0
C1D B:HEM602 3.1 24.3 1.0
C1B B:HEM602 3.1 21.0 1.0
C1A B:HEM602 3.1 18.6 1.0
C4A B:HEM602 3.1 23.2 1.0
C4C B:HEM602 3.1 24.8 1.0
CHA B:HEM602 3.4 23.9 1.0
CHC B:HEM602 3.4 27.7 1.0
CHD B:HEM602 3.4 25.8 1.0
CHB B:HEM602 3.4 17.9 1.0
CE2 B:TYR349 3.7 22.9 1.0
CE1 B:TYR349 3.7 23.6 1.0
NE B:ARG345 4.1 21.5 1.0
NH2 B:ARG345 4.2 25.6 1.0
O B:HOH757 4.2 25.3 1.0
C3D B:HEM602 4.2 25.3 1.0
C3B B:HEM602 4.3 22.2 1.0
C2D B:HEM602 4.3 21.2 1.0
C2C B:HEM602 4.3 30.7 1.0
C2B B:HEM602 4.3 24.9 1.0
C3C B:HEM602 4.3 27.1 1.0
C3A B:HEM602 4.3 24.1 1.0
C2A B:HEM602 4.3 19.9 1.0
CZ B:ARG345 4.6 20.8 1.0
CG2 B:VAL65 4.7 22.1 1.0
CD2 B:HIS66 4.7 25.7 1.0
NE2 B:HIS66 4.7 23.6 1.0
CZ B:PHE152 4.7 22.4 1.0
CD2 B:TYR349 5.0 29.0 1.0
CD1 B:TYR349 5.0 21.8 1.0

Iron binding site 3 out of 4 in 6rjn

Go back to Iron Binding Sites List in 6rjn
Iron binding site 3 out of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


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 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe601

b:34.5
occ:1.00
FE C:HEM601 0.0 34.5 1.0
OH C:TYR349 1.9 22.7 1.0
NA C:HEM601 2.0 23.2 1.0
NB C:HEM601 2.0 20.0 1.0
ND C:HEM601 2.1 25.1 1.0
NC C:HEM601 2.2 27.9 1.0
CZ C:TYR349 2.9 24.3 1.0
C4A C:HEM601 3.0 22.2 1.0
C1B C:HEM601 3.0 24.4 1.0
C1D C:HEM601 3.1 21.9 1.0
C1A C:HEM601 3.1 26.0 1.0
C4C C:HEM601 3.1 26.8 1.0
C4D C:HEM601 3.1 18.9 1.0
C4B C:HEM601 3.1 26.3 1.0
C1C C:HEM601 3.2 27.9 1.0
CHB C:HEM601 3.3 21.2 1.0
CHD C:HEM601 3.4 24.6 1.0
CHA C:HEM601 3.5 27.5 1.0
CHC C:HEM601 3.6 29.2 1.0
CE1 C:TYR349 3.7 21.0 1.0
CE2 C:TYR349 3.8 26.7 1.0
NE C:ARG345 4.1 23.9 1.0
C3A C:HEM601 4.2 22.4 1.0
C2B C:HEM601 4.2 28.0 1.0
C2A C:HEM601 4.3 21.2 1.0
O C:HOH777 4.3 28.0 1.0
C3B C:HEM601 4.3 25.1 1.0
NH2 C:ARG345 4.3 25.8 1.0
C2D C:HEM601 4.3 22.9 1.0
C3C C:HEM601 4.3 29.4 1.0
C3D C:HEM601 4.3 17.9 1.0
C2C C:HEM601 4.3 27.5 1.0
CZ C:ARG345 4.6 19.2 1.0
CG2 C:VAL65 4.6 24.8 1.0
CZ C:PHE152 4.6 26.9 1.0
CD2 C:HIS66 4.7 25.4 1.0
NE2 C:HIS66 4.8 22.4 1.0
CD1 C:TYR349 4.9 29.9 1.0
CD C:ARG345 5.0 24.9 1.0
CD2 C:TYR349 5.0 25.1 1.0

Iron binding site 4 out of 4 in 6rjn

Go back to Iron Binding Sites List in 6rjn
Iron binding site 4 out of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms


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 2.3 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe604

b:32.7
occ:1.00
FE D:HEM604 0.0 32.7 1.0
OH D:TYR349 1.8 21.7 1.0
NA D:HEM604 2.0 22.6 1.0
ND D:HEM604 2.0 25.8 1.0
NC D:HEM604 2.1 34.0 1.0
NB D:HEM604 2.1 29.5 1.0
CZ D:TYR349 2.9 21.1 1.0
C1D D:HEM604 3.0 26.4 1.0
C4C D:HEM604 3.0 28.9 1.0
C4A D:HEM604 3.0 24.1 1.0
C1A D:HEM604 3.1 19.0 1.0
C4D D:HEM604 3.1 23.0 1.0
C1C D:HEM604 3.1 23.8 1.0
C1B D:HEM604 3.1 24.5 1.0
C4B D:HEM604 3.2 26.1 1.0
CHD D:HEM604 3.3 24.7 1.0
CHB D:HEM604 3.4 16.6 1.0
CHA D:HEM604 3.5 20.8 1.0
CHC D:HEM604 3.5 23.3 1.0
CE1 D:TYR349 3.7 19.9 1.0
CE2 D:TYR349 3.8 19.9 1.0
NE D:ARG345 4.0 29.3 1.0
NH2 D:ARG345 4.2 24.0 1.0
C3A D:HEM604 4.2 24.5 1.0
C2D D:HEM604 4.2 24.6 1.0
C3C D:HEM604 4.2 28.5 1.0
C2A D:HEM604 4.3 24.5 1.0
O D:HOH820 4.3 32.4 1.0
C2C D:HEM604 4.3 27.3 1.0
C3D D:HEM604 4.3 24.0 1.0
C3B D:HEM604 4.4 23.9 1.0
C2B D:HEM604 4.4 20.8 1.0
CZ D:ARG345 4.5 26.4 1.0
CZ D:PHE152 4.6 27.5 1.0
NE2 D:HIS66 4.6 28.8 1.0
CD2 D:HIS66 4.7 29.0 1.0
CG2 D:VAL65 4.8 19.3 1.0
CD1 D:TYR349 4.9 17.2 1.0
CD D:ARG345 4.9 26.0 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 08:44:13 2024

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