Atomistry » Iron » PDB 5kja-5ktp » 5ksf
Atomistry »
  Iron »
    PDB 5kja-5ktp »
      5ksf »

Iron in PDB 5ksf: Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate

Enzymatic activity of Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate

All present enzymatic activity of Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate, PDB code: 5ksf was solved by P.C.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.38 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.692, 115.474, 174.586, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17.5

Other elements in 5ksf:

The structure of Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate (pdb code 5ksf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate, PDB code: 5ksf:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5ksf

Go back to Iron Binding Sites List in 5ksf
Iron binding site 1 out of 2 in the Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate


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 the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:22.1
occ:1.00
FE A:HEM801 0.0 22.1 1.0
ND A:HEM801 1.9 21.3 1.0
NA A:HEM801 2.0 25.8 1.0
NC A:HEM801 2.1 19.2 1.0
NB A:HEM801 2.1 24.9 1.0
NE2 A:HIS279 2.1 23.9 1.0
C4A A:HEM801 3.0 26.2 1.0
C1A A:HEM801 3.0 22.1 1.0
C1D A:HEM801 3.0 19.1 1.0
C1C A:HEM801 3.0 20.3 1.0
C4D A:HEM801 3.0 21.5 1.0
O A:ACT805 3.1 41.0 1.0
C4C A:HEM801 3.1 18.6 1.0
C1B A:HEM801 3.1 25.1 1.0
C4B A:HEM801 3.1 21.7 1.0
CE1 A:HIS279 3.1 21.7 1.0
CD2 A:HIS279 3.2 20.9 1.0
CHB A:HEM801 3.4 26.4 1.0
CHA A:HEM801 3.4 22.2 1.0
CHC A:HEM801 3.4 21.4 1.0
CHD A:HEM801 3.4 19.1 1.0
C A:ACT805 3.9 43.8 1.0
C3A A:HEM801 4.2 24.3 1.0
C3D A:HEM801 4.2 20.1 1.0
C2A A:HEM801 4.2 24.5 1.0
C2D A:HEM801 4.2 19.5 1.0
C2C A:HEM801 4.2 18.5 1.0
ND1 A:HIS279 4.2 23.8 1.0
C3C A:HEM801 4.2 19.5 1.0
NE1 A:TRP111 4.3 22.8 1.0
CG A:HIS279 4.3 23.4 1.0
C2B A:HEM801 4.3 27.0 1.0
C3B A:HEM801 4.4 23.4 1.0
OXT A:ACT805 4.5 51.2 1.0
CD1 A:TRP111 4.5 21.4 1.0
O1 A:OXY804 4.6 47.4 1.0
CH3 A:ACT805 4.9 45.0 1.0

Iron binding site 2 out of 2 in 5ksf

Go back to Iron Binding Sites List in 5ksf
Iron binding site 2 out of 2 in the Crystal Structure of the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate


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 the D141A Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:20.3
occ:1.00
FE B:HEM801 0.0 20.3 1.0
NA B:HEM801 2.0 19.9 1.0
NC B:HEM801 2.0 19.8 1.0
ND B:HEM801 2.0 18.8 1.0
NB B:HEM801 2.0 18.7 1.0
NE2 B:HIS279 2.1 20.6 1.0
OXT B:ACT805 2.9 35.9 1.0
C4D B:HEM801 3.0 16.6 1.0
C1A B:HEM801 3.0 18.4 1.0
C4A B:HEM801 3.0 20.3 1.0
C4B B:HEM801 3.0 18.7 1.0
C4C B:HEM801 3.0 20.5 1.0
C1C B:HEM801 3.0 19.4 1.0
C1D B:HEM801 3.0 18.8 1.0
C1B B:HEM801 3.0 21.7 1.0
CD2 B:HIS279 3.1 19.8 1.0
CE1 B:HIS279 3.2 20.8 1.0
CHD B:HEM801 3.4 19.8 1.0
CHB B:HEM801 3.4 21.6 1.0
CHA B:HEM801 3.4 18.3 1.0
CHC B:HEM801 3.4 18.3 1.0
C B:ACT805 3.9 33.9 1.0
C2A B:HEM801 4.2 21.3 1.0
C3A B:HEM801 4.2 20.5 1.0
C3B B:HEM801 4.2 20.6 1.0
C2C B:HEM801 4.2 17.9 1.0
C2D B:HEM801 4.2 16.6 1.0
C3D B:HEM801 4.2 17.6 1.0
C2B B:HEM801 4.3 20.5 1.0
C3C B:HEM801 4.3 18.6 1.0
ND1 B:HIS279 4.3 20.5 1.0
CG B:HIS279 4.3 19.6 1.0
NE1 B:TRP111 4.3 20.0 1.0
O B:ACT805 4.4 42.1 1.0
CD1 B:TRP111 4.5 20.5 1.0
O1 B:OXY804 4.7 37.6 1.0
CH3 B:ACT805 4.9 39.3 1.0

Reference:

M.Machuqueiro, B.Victor, J.Switala, J.Villanueva, C.Rovira, I.Fita, P.C.Loewen. The Catalase Activity of Catalase-Peroxidases Is Modulated By Changes in the Pka of the Distal Histidine. Biochemistry V. 56 2271 2017.
ISSN: ISSN 1520-4995
PubMed: 28409923
DOI: 10.1021/ACS.BIOCHEM.6B01276
Page generated: Sun Dec 13 16:06:09 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy