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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: Tue Dec 15 11:11:16 2020

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