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Iron in PDB 5v53: Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound

Enzymatic activity of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound

All present enzymatic activity of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound, PDB code: 5v53 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) 46.23 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.842, 115.825, 174.775, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 17.2

Other elements in 5v53:

The structure of Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound 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/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound (pdb code 5v53). 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/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound, PDB code: 5v53:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 5v53

Go back to Iron Binding Sites List in 5v53
Iron binding site 1 out of 2 in the Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound


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/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe801

b:19.2
occ:1.00
 FE A:HEM801 0.0 19.2 1.0
ND A:HEM801 2.0 18.6 1.0
NB A:HEM801 2.1 19.8 1.0
NA A:HEM801 2.1 22.1 1.0
NC A:HEM801 2.1 17.3 1.0
NE2 A:HIS279 2.1 21.1 1.0
C4A A:HEM801 3.0 22.5 1.0
C4D A:HEM801 3.0 17.6 1.0
C4B A:HEM801 3.0 20.2 1.0
O A:ACT805 3.1 31.3 0.6
C1D A:HEM801 3.1 18.1 1.0
C4C A:HEM801 3.1 16.1 1.0
C1C A:HEM801 3.1 18.7 1.0
C1B A:HEM801 3.1 21.1 1.0
C1A A:HEM801 3.1 18.3 1.0
CE1 A:HIS279 3.1 20.5 1.0
CD2 A:HIS279 3.2 18.6 1.0
CHC A:HEM801 3.4 17.4 1.0
CHA A:HEM801 3.4 19.7 1.0
CHB A:HEM801 3.4 21.0 1.0
CHD A:HEM801 3.5 16.9 1.0
C A:ACT805 3.9 31.8 0.6
C3D A:HEM801 4.2 17.7 1.0
C2D A:HEM801 4.3 16.6 1.0
ND1 A:HIS279 4.3 20.6 1.0
C3A A:HEM801 4.3 21.7 1.0
C2A A:HEM801 4.3 21.7 1.0
C3C A:HEM801 4.3 16.6 1.0
C2B A:HEM801 4.3 23.1 1.0
NE1 A:TRP111 4.3 20.5 1.0
C2C A:HEM801 4.3 16.7 1.0
CG A:HIS279 4.3 20.3 1.0
C3B A:HEM801 4.3 20.7 1.0
OXT A:ACT805 4.4 29.5 0.6
CD1 A:TRP111 4.5 18.6 1.0
O1 A:OXY804 4.6 40.3 1.0
CH3 A:ACT805 4.8 33.6 0.6

Iron binding site 2 out of 2 in 5v53

Go back to Iron Binding Sites List in 5v53
Iron binding site 2 out of 2 in the Crystal Structure of the D141A/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound


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/Q233E/N240D Variant of Catalase- Peroxidase From B. Pseudomallei with Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:18.8
occ:1.00
 FE B:HEM801 0.0 18.8 1.0
NA B:HEM801 2.0 18.4 1.0
ND B:HEM801 2.0 19.4 1.0
NC B:HEM801 2.0 16.8 1.0
NB B:HEM801 2.1 18.3 1.0
NE2 B:HIS279 2.1 19.5 1.0
C1C B:HEM801 3.0 16.1 1.0
OXT B:ACT805 3.0 34.3 0.6
C1A B:HEM801 3.0 18.6 1.0
C1B B:HEM801 3.0 18.0 1.0
C4D B:HEM801 3.0 17.5 1.0
C1D B:HEM801 3.0 16.9 1.0
C4B B:HEM801 3.1 18.3 1.0
C4C B:HEM801 3.1 17.5 1.0
C4A B:HEM801 3.1 19.2 1.0
CE1 B:HIS279 3.1 17.7 1.0
CD2 B:HIS279 3.1 18.6 1.0
CHA B:HEM801 3.4 17.1 1.0
CHC B:HEM801 3.4 17.8 1.0
CHB B:HEM801 3.4 18.3 1.0
CHD B:HEM801 3.4 16.2 1.0
C B:ACT805 3.9 27.3 0.6
C3D B:HEM801 4.2 17.7 1.0
C2C B:HEM801 4.2 16.5 1.0
C3C B:HEM801 4.3 17.5 1.0
O B:ACT805 4.3 28.5 0.6
C2B B:HEM801 4.3 19.0 1.0
C2D B:HEM801 4.3 16.9 1.0
C2A B:HEM801 4.3 18.6 1.0
C3B B:HEM801 4.3 18.8 1.0
C3A B:HEM801 4.3 19.6 1.0
ND1 B:HIS279 4.3 19.5 1.0
NE1 B:TRP111 4.3 18.7 1.0
CG B:HIS279 4.3 18.0 1.0
CD1 B:TRP111 4.5 18.8 1.0
O1 B:OXY804 4.7 34.3 1.0
CH3 B:ACT805 4.7 26.0 0.6

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: Tue Aug 6 10:13:13 2024

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