Atomistry » Sodium » PDB 5kd8-5kw9 » 5ksf
Atomistry »
  Sodium »
    PDB 5kd8-5kw9 »
      5ksf »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy