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Sodium in PDB 5kt8: Crystal Structure of the W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid

Enzymatic activity of Crystal Structure of the W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid

All present enzymatic activity of Crystal Structure of the W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid, PDB code: 5kt8 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) 48.36 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.651, 112.782, 174.539, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.6

Other elements in 5kt8:

The structure of Crystal Structure of the W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid 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 W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid (pdb code 5kt8). 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 W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid, PDB code: 5kt8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5kt8

Go back to Sodium Binding Sites List in 5kt8
Sodium binding site 1 out of 2 in the Crystal Structure of the W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid


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 W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:25.4
occ:1.00
 O A:GLY124 2.3 21.9 1.0
O A:GLY122 2.3 22.3 1.0
O A:HOH1102 2.4 26.8 1.0
O A:SER494 2.4 25.3 1.0
O A:HOH1373 2.4 28.7 1.0
C A:SER494 3.3 23.9 1.0
C A:GLY124 3.4 23.9 1.0
C A:GLY122 3.5 22.2 1.0
C A:ARG123 3.5 24.2 1.0
CA A:ARG123 3.5 22.6 1.0
N A:GLY124 3.6 23.8 1.0
O A:HOH1402 3.9 24.4 1.0
N A:ARG123 4.0 22.4 1.0
CA A:SER494 4.0 23.2 1.0
OD2 A:ASP427 4.1 24.3 1.0
CA A:GLY124 4.1 23.6 1.0
O A:ARG123 4.1 24.8 1.0
N A:ASP495 4.1 24.1 1.0
O A:HOH1070 4.1 34.8 1.0
CB A:ASP427 4.1 23.9 1.0
CB A:SER494 4.2 22.2 1.0
CA A:ASP495 4.4 25.9 1.0
N A:GLY125 4.6 23.7 1.0
CB A:ASP495 4.6 23.9 1.0
CL A:CL803 4.6 43.0 1.0
CD1 A:TYR117 4.6 24.3 1.0
CG A:ASP427 4.6 24.1 1.0
CA A:GLY122 4.8 23.0 1.0
CB A:ARG123 4.8 23.7 1.0
CE1 A:TYR117 4.9 22.0 1.0
CA A:GLY125 4.9 23.8 1.0

Sodium binding site 2 out of 2 in 5kt8

Go back to Sodium Binding Sites List in 5kt8
Sodium binding site 2 out of 2 in the Crystal Structure of the W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid


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 W139F Variant of the Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:24.6
occ:1.00
 O B:HOH1341 2.3 25.4 1.0
O B:GLY122 2.3 23.1 1.0
O B:GLY124 2.4 24.7 1.0
O B:SER494 2.4 24.6 1.0
O B:HOH1054 2.4 22.2 1.0
C B:SER494 3.1 22.1 1.0
C B:GLY122 3.4 21.4 1.0
C B:GLY124 3.5 22.1 1.0
CA B:ARG123 3.6 20.0 1.0
C B:ARG123 3.6 21.2 1.0
N B:GLY124 3.6 21.1 1.0
CA B:SER494 3.9 21.9 1.0
N B:ARG123 3.9 20.4 1.0
N B:ASP495 4.0 22.6 1.0
O B:HOH1407 4.0 27.2 1.0
CB B:SER494 4.1 21.5 1.0
O B:ARG123 4.1 21.0 1.0
OD2 B:ASP427 4.1 25.2 1.0
CA B:GLY124 4.2 21.6 1.0
CB B:ASP427 4.2 24.2 1.0
O B:HOH1092 4.3 34.1 1.0
CA B:ASP495 4.4 23.1 1.0
CB B:ASP495 4.5 23.4 1.0
CD1 B:TYR117 4.6 24.5 1.0
CL B:CL803 4.6 36.5 1.0
N B:GLY125 4.6 22.9 1.0
CA B:GLY122 4.7 22.9 1.0
CG B:ASP427 4.7 24.9 1.0
CE1 B:TYR117 4.8 23.5 1.0
CB B:ARG123 4.8 20.7 1.0
OE2 B:GLU128 4.9 36.4 1.0
OG B:SER494 4.9 22.1 1.0

Reference:

P.C.Loewen, P.C.Loewen. N/A N/A.
Page generated: Mon Oct 7 22:10:37 2024

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