Atomistry » Sodium » PDB 5rdl-5syk » 5sx7
Atomistry »
  Sodium »
    PDB 5rdl-5syk »
      5sx7 »

Sodium in PDB 5sx7: Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5

Enzymatic activity of Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5

All present enzymatic activity of Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5, PDB code: 5sx7 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) 20.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.413, 114.948, 173.998, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 18.9

Other elements in 5sx7:

The structure of Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5 also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5 (pdb code 5sx7). 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 Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5, PDB code: 5sx7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5sx7

Go back to Sodium Binding Sites List in 5sx7
Sodium binding site 1 out of 2 in the Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5


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 Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:20.2
occ:1.00
O A:GLY124 2.3 17.2 1.0
O A:SER494 2.4 14.9 1.0
O A:HOH1386 2.4 33.0 1.0
O A:HOH1023 2.4 21.0 1.0
O A:GLY122 2.4 17.5 1.0
C A:SER494 3.3 14.9 1.0
C A:GLY124 3.5 15.4 1.0
C A:GLY122 3.6 16.2 1.0
N A:GLY124 3.6 14.5 1.0
C A:ARG123 3.6 14.9 1.0
CA A:ARG123 3.7 15.0 1.0
O A:HOH1032 3.8 35.7 1.0
O A:HOH1182 3.8 15.4 1.0
OD2 A:ASP427 3.9 18.3 1.0
CB A:ASP427 4.0 17.9 1.0
CA A:SER494 4.0 13.6 1.0
N A:ARG123 4.1 14.8 1.0
N A:ASP495 4.1 14.5 1.0
CA A:GLY124 4.2 16.1 1.0
O A:ARG123 4.2 13.4 1.0
CB A:SER494 4.3 14.0 1.0
CA A:ASP495 4.4 14.6 1.0
CG A:ASP427 4.5 18.8 1.0
N A:GLY125 4.6 15.3 1.0
CB A:ASP495 4.6 14.4 1.0
CD1 A:TYR117 4.7 16.3 1.0
CA A:GLY122 4.9 15.7 1.0
CA A:GLY125 4.9 14.6 1.0
CE1 A:TYR117 4.9 16.5 1.0
OE2 A:GLU198 4.9 23.5 1.0
CB A:ARG123 5.0 14.9 1.0

Sodium binding site 2 out of 2 in 5sx7

Go back to Sodium Binding Sites List in 5sx7
Sodium binding site 2 out of 2 in the Crystal Structure of Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5


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 Catalase-Peroxidase Katg of B. Pseudomallei at pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na803

b:16.8
occ:1.00
O B:GLY124 2.3 12.9 1.0
O B:SER494 2.3 15.7 1.0
O B:GLY122 2.3 12.9 1.0
O B:HOH1051 2.4 17.6 1.0
O B:HOH1005 2.4 29.4 1.0
C B:SER494 3.2 14.4 1.0
C B:GLY122 3.5 13.0 1.0
C B:GLY124 3.5 12.7 1.0
C B:ARG123 3.6 12.9 1.0
N B:GLY124 3.7 13.7 1.0
CA B:ARG123 3.7 12.4 1.0
CA B:SER494 3.9 12.3 1.0
O B:HOH1234 4.0 17.8 1.0
N B:ARG123 4.0 12.7 1.0
N B:ASP495 4.0 13.4 1.0
O B:HOH1010 4.1 28.8 1.0
CB B:ASP427 4.1 15.2 1.0
OD2 B:ASP427 4.1 18.2 1.0
CB B:SER494 4.1 12.1 1.0
CA B:GLY124 4.2 12.8 1.0
O B:ARG123 4.2 12.1 1.0
OE2 B:GLU128 4.4 40.1 1.0
CA B:ASP495 4.4 13.5 1.0
CB B:ASP495 4.6 13.8 1.0
CG B:ASP427 4.6 16.6 1.0
N B:GLY125 4.6 11.9 1.0
CD1 B:TYR117 4.7 13.7 1.0
CA B:GLY122 4.8 12.9 1.0
OE2 B:GLU198 4.8 25.1 1.0
CE1 B:TYR117 4.9 13.0 1.0
OG B:SER494 4.9 11.9 1.0
CA B:GLY125 5.0 12.3 1.0
CB B:ARG123 5.0 12.2 1.0

Reference:

X.Carpena, B.Wiseman, T.Deemagarn, B.Herguedas, A.Ivancich, R.Singh, P.C.Loewen, I.Fita. Roles For ARG426 and TRP111 in the Modulation of Nadh Oxidase Activity of the Catalase-Peroxidase Katg From Burkholderia Pseudomallei Inferred From pH-Induced Structural Changes. Biochemistry V. 45 5171 2006.
ISSN: ISSN 0006-2960
PubMed: 16618106
Page generated: Tue Dec 15 11:33:57 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy