Atomistry » Iron » PDB 5utd-5ve3 » 5v53
Atomistry »
  Iron »
    PDB 5utd-5ve3 »
      5v53 »

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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy