Iron in PDB 5kqh: Crystal Structure of the V293D Variant of Catalase-Peroxidase From B. Pseudomallei

All present enzymatic activity of Crystal Structure of the V293D Variant of Catalase-Peroxidase From B. Pseudomallei:
1.11.1.21;

The structure of Crystal Structure of the V293D Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kqh 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)	47.56 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.787, 113.434, 174.677, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18.4

The structure of Crystal Structure of the V293D Variant of Catalase-Peroxidase From B. Pseudomallei also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Iron atom in the Crystal Structure of the V293D Variant of Catalase-Peroxidase From B. Pseudomallei (pdb code 5kqh). 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 V293D Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kqh:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of the V293D Variant of Catalase-Peroxidase From B. Pseudomallei


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 V293D Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:16.0 occ:1.00 FE A:HEM801 0.0 16.0 1.0 ND A:HEM801 2.0 14.7 1.0 NB A:HEM801 2.1 16.4 1.0 NA A:HEM801 2.1 17.5 1.0 NC A:HEM801 2.1 14.9 1.0 NE2 A:HIS279 2.1 16.6 1.0 O2 A:TOX111 2.6 27.7 0.8 C1D A:HEM801 3.0 13.6 1.0 C4D A:HEM801 3.0 14.2 1.0 C1B A:HEM801 3.0 16.9 1.0 C1A A:HEM801 3.0 15.9 1.0 C1C A:HEM801 3.0 14.8 1.0 C4B A:HEM801 3.1 16.6 1.0 CE1 A:HIS279 3.1 15.6 1.0 C4C A:HEM801 3.1 14.3 1.0 C4A A:HEM801 3.1 17.6 1.0 CD2 A:HIS279 3.1 16.4 1.0 CHA A:HEM801 3.4 15.3 1.0 CHC A:HEM801 3.4 15.2 1.0 CHD A:HEM801 3.4 12.9 1.0 CHB A:HEM801 3.4 16.0 1.0 O1 A:TOX111 3.6 21.7 0.9 ND1 A:HIS279 4.2 15.5 1.0 C2B A:HEM801 4.2 17.0 1.0 C3D A:HEM801 4.2 14.4 1.0 C2D A:HEM801 4.2 13.4 1.0 CG A:HIS279 4.3 16.3 1.0 NE1 A:TOX111 4.3 18.1 1.0 C3C A:HEM801 4.3 14.5 1.0 C2C A:HEM801 4.3 13.5 1.0 C2A A:HEM801 4.3 18.4 1.0 O1 A:OXY804 4.3 37.9 1.0 C3B A:HEM801 4.3 17.3 1.0 C3A A:HEM801 4.3 17.3 1.0 O2 A:TOX111 4.4 18.6 0.1 CD1 A:TOX111 4.4 16.5 1.0 O A:HOH967 5.0 29.0 1.0

Iron binding site 2 out of 2 in the Crystal Structure of the V293D Variant of Catalase-Peroxidase From B. Pseudomallei


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 V293D Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:15.5 occ:1.00 FE B:HEM801 0.0 15.5 1.0 ND B:HEM801 2.0 14.6 1.0 NC B:HEM801 2.0 14.2 1.0 NA B:HEM801 2.0 13.9 1.0 NB B:HEM801 2.1 15.4 1.0 NE2 B:HIS279 2.1 19.2 1.0 O2 B:TOX111 2.8 22.6 0.8 C1C B:HEM801 3.0 15.4 1.0 C1A B:HEM801 3.0 14.0 1.0 C4D B:HEM801 3.0 13.5 1.0 C4B B:HEM801 3.0 14.1 1.0 C1D B:HEM801 3.0 14.1 1.0 C4C B:HEM801 3.1 14.2 1.0 CE1 B:HIS279 3.1 17.8 1.0 C1B B:HEM801 3.1 15.2 1.0 C4A B:HEM801 3.1 15.1 1.0 CD2 B:HIS279 3.1 18.9 1.0 CHC B:HEM801 3.3 14.3 1.0 CHA B:HEM801 3.3 13.8 1.0 CHB B:HEM801 3.5 15.2 1.0 CHD B:HEM801 3.5 14.2 1.0 O1 B:TOX111 3.6 22.8 1.0 C3D B:HEM801 4.2 14.6 1.0 C2A B:HEM801 4.2 13.7 1.0 C2D B:HEM801 4.2 13.9 1.0 ND1 B:HIS279 4.2 17.5 1.0 C3A B:HEM801 4.2 14.0 1.0 C3B B:HEM801 4.3 15.7 1.0 O2 B:TOX111 4.3 17.9 0.2 C2C B:HEM801 4.3 15.1 1.0 CG B:HIS279 4.3 18.8 1.0 NE1 B:TOX111 4.3 18.2 1.0 C2B B:HEM801 4.3 15.8 1.0 O1 B:OXY803 4.3 30.4 1.0 C3C B:HEM801 4.3 14.3 1.0 CD1 B:TOX111 4.5 17.8 1.0 O B:HOH917 4.9 30.5 1.0

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