Atomistry » Sodium » PDB 5kd8-5kw9 » 5kt9
Atomistry »
  Sodium »
    PDB 5kd8-5kw9 »
      5kt9 »

Sodium in PDB 5kt9: Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide

Enzymatic activity of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide

All present enzymatic activity of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide, PDB code: 5kt9 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) 50.00 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.854, 113.790, 174.633, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.3

Other elements in 5kt9:

The structure of Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide 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 Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide (pdb code 5kt9). 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 Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide, PDB code: 5kt9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5kt9

Go back to Sodium Binding Sites List in 5kt9
Sodium binding site 1 out of 2 in the Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide


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 Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:22.9
occ:1.00
 O A:GLY124 2.3 21.8 1.0
O A:GLY122 2.4 20.5 1.0
O A:HOH1465 2.4 21.5 1.0
O A:SER494 2.5 23.3 1.0
O A:HOH1229 2.5 22.4 1.0
C A:SER494 3.3 22.3 1.0
C A:GLY124 3.4 19.9 1.0
C A:GLY122 3.5 18.7 1.0
N A:GLY124 3.6 20.2 1.0
C A:ARG123 3.6 22.3 1.0
CA A:ARG123 3.6 20.4 1.0
N A:ARG123 4.0 20.0 1.0
CA A:SER494 4.1 20.3 1.0
OD2 A:ASP427 4.1 23.6 1.0
O A:HOH1035 4.1 32.2 1.0
CA A:GLY124 4.1 21.2 1.0
O A:HOH1510 4.1 23.3 1.0
O A:ARG123 4.1 20.4 1.0
CB A:ASP427 4.1 24.8 1.0
N A:ASP495 4.2 21.0 1.0
CB A:SER494 4.2 20.1 1.0
CA A:ASP495 4.5 20.8 1.0
N A:GLY125 4.5 21.1 1.0
CL A:CL803 4.5 40.4 1.0
CD1 A:TYR117 4.6 22.2 1.0
CG A:ASP427 4.7 27.1 1.0
CB A:ASP495 4.7 21.8 1.0
CA A:GLY122 4.8 19.2 1.0
CA A:GLY125 4.8 17.0 1.0
CE1 A:TYR117 4.9 22.2 1.0
CB A:ARG123 4.9 21.0 1.0

Sodium binding site 2 out of 2 in 5kt9

Go back to Sodium Binding Sites List in 5kt9
Sodium binding site 2 out of 2 in the Crystal Structure of the Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide


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 Catalase-Peroxidase From B. Pseudomallei Treated with Hydrogen Peroxide and Carbon Monoxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na803

b:22.5
occ:1.00
 O B:HOH1438 2.3 25.1 1.0
O B:GLY124 2.4 22.6 1.0
O B:GLY122 2.4 20.3 1.0
O B:HOH1020 2.5 28.3 1.0
O B:SER494 2.5 21.6 1.0
C B:SER494 3.3 21.0 1.0
C B:GLY122 3.5 18.3 1.0
C B:GLY124 3.5 19.5 1.0
C B:ARG123 3.6 20.1 1.0
CA B:ARG123 3.6 17.7 1.0
N B:GLY124 3.6 20.0 1.0
O B:HOH1435 3.8 26.2 1.0
N B:ARG123 4.0 19.0 1.0
O B:HOH1025 4.0 34.0 1.0
CA B:SER494 4.0 22.0 1.0
OD2 B:ASP427 4.1 20.8 1.0
O B:ARG123 4.1 16.7 1.0
CA B:GLY124 4.1 20.2 1.0
N B:ASP495 4.1 20.8 1.0
CB B:SER494 4.2 19.6 1.0
CB B:ASP427 4.2 22.1 1.0
CA B:ASP495 4.5 20.2 1.0
CD1 B:TYR117 4.6 18.4 1.0
CL B:CL804 4.6 36.8 1.0
N B:GLY125 4.6 20.1 1.0
CB B:ASP495 4.7 20.5 1.0
CG B:ASP427 4.7 21.9 1.0
CA B:GLY122 4.8 19.7 1.0
O B:HOH1446 4.8 40.9 1.0
CB B:ARG123 4.8 18.6 1.0
CE1 B:TYR117 4.9 19.0 1.0
CA B:GLY125 4.9 20.5 1.0
OG B:SER494 5.0 19.9 1.0

Reference:

P.C.Loewen, P.C.Loewen. N/A N/A.
Page generated: Mon Oct 7 22:10:42 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy