Atomistry » Iron » PDB 6r6m-6rsj » 6rjn
Atomistry »
  Iron »
    PDB 6r6m-6rsj »
      6rjn »

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: Sun Dec 13 17:02:52 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy