Atomistry » Sodium » PDB 5k9h-5ku9 » 5ksg
Atomistry »
  Sodium »
    PDB 5k9h-5ku9 »
      5ksg »

Sodium in PDB 5ksg: Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid

Enzymatic activity of Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid

All present enzymatic activity of Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid, PDB code: 5ksg 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) 96.54 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.665, 115.928, 174.349, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 15.9

Other elements in 5ksg:

The structure of Crystal Structure of the W153F Variant of 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 W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid (pdb code 5ksg). 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 W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid, PDB code: 5ksg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ksg

Go back to Sodium Binding Sites List in 5ksg
Sodium binding site 1 out of 2 in the Crystal Structure of the W153F Variant of 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 W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:14.5
occ:1.00
O A:GLY124 2.3 13.5 1.0
O A:HOH1532 2.3 18.8 1.0
O A:HOH968 2.4 17.5 1.0
O A:SER494 2.4 15.0 1.0
O A:GLY122 2.4 13.6 1.0
C A:SER494 3.2 15.0 1.0
C A:GLY124 3.4 14.1 1.0
C A:GLY122 3.5 12.8 1.0
N A:GLY124 3.6 13.1 1.0
C A:ARG123 3.6 12.5 1.0
CA A:ARG123 3.6 12.5 1.0
O A:HOH1595 3.9 18.9 1.0
CA A:SER494 3.9 13.3 1.0
OD2 A:ASP427 4.0 15.3 1.0
N A:ARG123 4.0 13.1 1.0
O A:HOH1072 4.0 30.5 1.0
N A:ASP495 4.1 13.2 1.0
CA A:GLY124 4.1 13.6 1.0
CB A:ASP427 4.2 15.4 1.0
CB A:SER494 4.2 14.2 1.0
O A:ARG123 4.2 13.5 1.0
CA A:ASP495 4.4 13.4 1.0
N A:GLY125 4.5 12.0 1.0
CL A:CL803 4.6 29.3 1.0
CG A:ASP427 4.6 17.2 1.0
CB A:ASP495 4.6 13.3 1.0
CD1 A:TYR117 4.7 13.9 1.0
OE2 A:GLU128 4.7 28.6 1.0
CA A:GLY122 4.8 13.4 1.0
CA A:GLY125 4.9 12.9 1.0
CB A:ARG123 4.9 14.7 1.0
OG A:SER494 5.0 13.3 1.0
CE1 A:TYR117 5.0 13.2 1.0

Sodium binding site 2 out of 2 in 5ksg

Go back to Sodium Binding Sites List in 5ksg
Sodium binding site 2 out of 2 in the Crystal Structure of the W153F Variant of 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 W153F Variant of Catalase-Peroxidase From B. Pseudomallei Treated with Isoniazid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:14.9
occ:1.00
O B:HOH1529 2.3 18.7 1.0
O B:GLY124 2.3 13.7 1.0
O B:GLY122 2.4 12.1 1.0
O B:SER494 2.4 14.3 1.0
O B:HOH987 2.4 16.9 1.0
C B:SER494 3.3 15.2 1.0
C B:GLY124 3.5 13.9 1.0
C B:GLY122 3.5 12.1 1.0
N B:GLY124 3.6 13.8 1.0
C B:ARG123 3.6 12.8 1.0
CA B:ARG123 3.6 12.7 1.0
CA B:SER494 3.9 13.4 1.0
O B:HOH1600 3.9 17.2 1.0
OD2 B:ASP427 4.0 17.4 1.0
N B:ARG123 4.0 12.9 1.0
O B:HOH1218 4.1 28.4 1.0
CB B:SER494 4.1 12.9 1.0
CA B:GLY124 4.1 12.9 1.0
N B:ASP495 4.2 13.0 1.0
O B:ARG123 4.2 12.4 1.0
CB B:ASP427 4.2 17.0 1.0
CA B:ASP495 4.5 13.1 1.0
CL B:CL803 4.6 26.4 1.0
N B:GLY125 4.6 11.3 1.0
CB B:ASP495 4.6 13.4 1.0
OE2 B:GLU128 4.7 27.8 1.0
CD1 B:TYR117 4.7 13.1 1.0
CG B:ASP427 4.7 17.6 1.0
CA B:GLY122 4.8 12.5 1.0
CA B:GLY125 4.9 12.8 1.0
CB B:ARG123 4.9 13.2 1.0
OG B:SER494 4.9 14.0 1.0
CE1 B:TYR117 5.0 12.5 1.0

Reference:

P.C.Loewen, P.C.Loewen. N/A N/A.
Page generated: Tue Dec 15 11:11:08 2020

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy