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

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

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

Protein crystallography data

The structure of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Acetate, PDB code: 5ksk 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) 48.39 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.703, 115.480, 174.966, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 18

Other elements in 5ksk:

The structure of Crystal Structure 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 Catalase-Peroxidase From B. Pseudomallei Treated with Acetate (pdb code 5ksk). 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 Catalase-Peroxidase From B. Pseudomallei Treated with Acetate, PDB code: 5ksk:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5ksk

Go back to Iron Binding Sites List in 5ksk
Iron binding site 1 out of 2 in the Crystal Structure 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 Catalase-Peroxidase From B. Pseudomallei Treated with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:19.5
occ:1.00
FE A:HEM801 0.0 19.5 1.0
ND A:HEM801 1.9 20.5 1.0
NA A:HEM801 2.1 22.2 1.0
NE2 A:HIS279 2.1 18.9 1.0
NC A:HEM801 2.1 16.8 1.0
NB A:HEM801 2.1 19.7 1.0
O2 A:TOX111 2.8 25.1 0.8
C4A A:HEM801 3.0 22.6 1.0
C1D A:HEM801 3.0 19.0 1.0
C4C A:HEM801 3.1 17.5 1.0
C4B A:HEM801 3.1 19.4 1.0
C1C A:HEM801 3.1 17.9 1.0
C4D A:HEM801 3.1 18.3 1.0
C1A A:HEM801 3.1 20.0 1.0
C1B A:HEM801 3.1 21.0 1.0
CE1 A:HIS279 3.1 18.2 1.0
CD2 A:HIS279 3.2 16.4 1.0
CHB A:HEM801 3.4 22.0 1.0
CHC A:HEM801 3.4 19.0 1.0
CHD A:HEM801 3.4 16.6 1.0
CHA A:HEM801 3.5 20.4 1.0
O1 A:TOX111 3.5 26.9 0.8
ND1 A:HIS279 4.2 19.2 1.0
NE1 A:TOX111 4.2 20.2 1.0
C3A A:HEM801 4.3 20.5 1.0
C2A A:HEM801 4.3 20.7 1.0
C2C A:HEM801 4.3 17.8 1.0
C2B A:HEM801 4.3 23.9 1.0
CG A:HIS279 4.3 18.6 1.0
C3D A:HEM801 4.3 18.5 1.0
C3C A:HEM801 4.3 17.6 1.0
C2D A:HEM801 4.3 17.7 1.0
C3B A:HEM801 4.4 20.3 1.0
O1 A:OXY804 4.4 42.5 1.0
CD1 A:TOX111 4.5 20.1 1.0
O A:HOH1074 4.9 37.9 1.0

Iron binding site 2 out of 2 in 5ksk

Go back to Iron Binding Sites List in 5ksk
Iron binding site 2 out of 2 in the Crystal Structure 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 Catalase-Peroxidase From B. Pseudomallei Treated with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:18.1
occ:1.00
FE B:HEM801 0.0 18.1 1.0
NC B:HEM801 2.0 16.1 1.0
NA B:HEM801 2.0 16.4 1.0
ND B:HEM801 2.0 18.0 1.0
NB B:HEM801 2.0 18.1 1.0
NE2 B:HIS279 2.2 20.2 1.0
O2 B:TOX111 2.7 21.6 0.7
C1C B:HEM801 3.0 15.5 1.0
C1A B:HEM801 3.0 16.9 1.0
C4D B:HEM801 3.0 16.3 1.0
C1D B:HEM801 3.0 16.3 1.0
C4A B:HEM801 3.0 17.1 1.0
C1B B:HEM801 3.1 18.1 1.0
C4B B:HEM801 3.1 17.0 1.0
C4C B:HEM801 3.1 17.7 1.0
CE1 B:HIS279 3.2 19.2 1.0
CD2 B:HIS279 3.2 18.7 1.0
CHA B:HEM801 3.4 17.1 1.0
CHD B:HEM801 3.4 16.3 1.0
CHC B:HEM801 3.4 16.6 1.0
CHB B:HEM801 3.5 18.0 1.0
O1 B:TOX111 3.6 22.6 0.8
O2 B:TOX111 4.2 18.0 0.1
C3C B:HEM801 4.2 15.5 1.0
C2D B:HEM801 4.2 16.2 1.0
NE1 B:TOX111 4.3 16.8 0.8
C2A B:HEM801 4.3 16.3 1.0
C2C B:HEM801 4.3 16.6 1.0
C3D B:HEM801 4.3 17.2 1.0
C3A B:HEM801 4.3 16.0 1.0
C2B B:HEM801 4.3 18.9 1.0
C3B B:HEM801 4.3 19.7 1.0
ND1 B:HIS279 4.3 18.5 1.0
CG B:HIS279 4.3 18.3 1.0
CD1 B:TOX111 4.5 17.5 1.0
O1 B:OXY804 4.6 36.4 1.0
O B:HOH954 4.8 36.3 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 16:06:12 2020

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