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Sodium 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:

Iron (Fe) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ksf

Go back to Sodium Binding Sites List in 5ksf
Sodium 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 Sodium with other atoms in the Na 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:Na802

b:22.9
occ:1.00
 O A:HOH1443 2.3 27.1 1.0
O A:GLY124 2.3 19.6 1.0
O A:SER494 2.4 23.0 1.0
O A:HOH1094 2.4 24.8 1.0
O A:GLY122 2.4 21.6 1.0
C A:SER494 3.2 21.1 1.0
C A:GLY124 3.4 22.0 1.0
C A:GLY122 3.6 20.4 1.0
N A:GLY124 3.6 18.9 1.0
C A:ARG123 3.6 19.4 1.0
CA A:ARG123 3.6 20.2 1.0
O A:HOH1492 3.8 25.4 1.0
OD2 A:ASP427 4.0 23.8 1.0
CA A:SER494 4.0 20.1 1.0
O A:HOH1089 4.0 36.3 1.0
N A:ARG123 4.1 18.7 1.0
CB A:ASP427 4.1 23.9 1.0
N A:ASP495 4.1 19.2 1.0
CA A:GLY124 4.1 19.8 1.0
O A:ARG123 4.2 20.4 1.0
CB A:SER494 4.2 21.1 1.0
CA A:ASP495 4.5 20.3 1.0
N A:GLY125 4.5 20.0 1.0
CL A:CL803 4.6 38.3 1.0
CG A:ASP427 4.6 27.1 1.0
CB A:ASP495 4.6 18.8 1.0
CD1 A:TYR117 4.6 22.4 1.0
CA A:GLY125 4.8 19.2 1.0
CA A:GLY122 4.9 20.2 1.0
CB A:ARG123 4.9 22.0 1.0
CE1 A:TYR117 4.9 21.5 1.0
OG A:SER494 5.0 20.1 1.0

Sodium binding site 2 out of 2 in 5ksf

Go back to Sodium Binding Sites List in 5ksf
Sodium 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 Sodium with other atoms in the Na 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:Na802

b:21.6
occ:1.00
 O B:HOH1457 2.3 24.8 1.0
O B:GLY122 2.4 17.7 1.0
O B:GLY124 2.4 19.8 1.0
O B:HOH948 2.4 25.5 1.0
O B:SER494 2.4 21.1 1.0
C B:SER494 3.2 21.8 1.0
C B:GLY124 3.5 19.7 1.0
C B:GLY122 3.5 17.4 1.0
N B:GLY124 3.6 20.5 1.0
C B:ARG123 3.6 19.5 1.0
CA B:ARG123 3.7 17.8 1.0
O B:HOH1493 3.9 24.5 1.0
OD2 B:ASP427 4.0 23.1 1.0
CA B:SER494 4.0 20.3 1.0
O B:HOH1027 4.0 36.3 1.0
N B:ARG123 4.1 17.2 1.0
N B:ASP495 4.1 20.2 1.0
CB B:ASP427 4.1 22.2 1.0
CB B:SER494 4.2 20.2 1.0
CA B:GLY124 4.2 19.7 1.0
O B:ARG123 4.2 18.6 1.0
CA B:ASP495 4.4 19.1 1.0
CB B:ASP495 4.6 19.1 1.0
CL B:CL803 4.6 37.8 1.0
N B:GLY125 4.6 18.2 1.0
CD1 B:TYR117 4.6 18.6 1.0
CG B:ASP427 4.7 22.4 1.0
CA B:GLY122 4.8 17.3 1.0
CA B:GLY125 4.9 19.6 1.0
CE1 B:TYR117 4.9 18.9 1.0
CB B:ARG123 4.9 17.7 1.0
OG B:SER494 5.0 19.8 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: Mon Oct 7 22:09:46 2024

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