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Sodium in PDB 5sxt: Crystal Structure of the S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound

Enzymatic activity of Crystal Structure of the S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound

All present enzymatic activity of Crystal Structure of the S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound, PDB code: 5sxt 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.220, 112.600, 173.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.7

Other elements in 5sxt:

The structure of Crystal Structure of the S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound 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 S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound (pdb code 5sxt). 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 S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound, PDB code: 5sxt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5sxt

Go back to Sodium Binding Sites List in 5sxt
Sodium binding site 1 out of 2 in the Crystal Structure of the S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound


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 S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:20.1
occ:1.00
 O A:GLY124 2.3 17.9 1.0
O A:GLY122 2.3 21.7 1.0
O A:SER494 2.3 18.7 1.0
O A:HOH1398 2.4 25.0 1.0
O A:HOH1095 2.5 28.0 1.0
C A:SER494 3.1 18.9 1.0
C A:GLY124 3.4 17.6 1.0
C A:GLY122 3.4 19.4 1.0
C A:ARG123 3.5 18.7 1.0
CA A:ARG123 3.5 18.9 1.0
N A:GLY124 3.6 18.8 1.0
CA A:SER494 3.9 18.2 1.0
N A:ARG123 4.0 19.1 1.0
N A:ASP495 4.0 18.7 1.0
O A:HOH1442 4.0 24.1 1.0
OD2 A:ASP427 4.0 22.5 1.0
CB A:SER494 4.1 18.5 1.0
CA A:GLY124 4.1 17.8 1.0
O A:ARG123 4.1 18.7 1.0
CB A:ASP427 4.1 20.6 1.0
O A:HOH1026 4.2 30.2 1.0
CA A:ASP495 4.4 18.2 1.0
N A:GLY125 4.6 17.6 1.0
CB A:ASP495 4.6 18.2 1.0
CL A:CL803 4.6 34.6 1.0
CG A:ASP427 4.6 22.2 1.0
CD1 A:TYR117 4.6 19.0 1.0
OE2 A:GLU128 4.7 32.1 1.0
CA A:GLY122 4.7 20.8 1.0
CB A:ARG123 4.9 19.1 1.0
CE1 A:TYR117 4.9 18.9 1.0
OG A:SER494 4.9 18.3 1.0
CA A:GLY125 4.9 16.7 1.0

Sodium binding site 2 out of 2 in 5sxt

Go back to Sodium Binding Sites List in 5sxt
Sodium binding site 2 out of 2 in the Crystal Structure of the S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound


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 S324T Variant of Burkholderia Pseudomallei Katg with Isonicotinic Acid Hydrazide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:18.2
occ:1.00
 O B:GLY124 2.3 18.1 1.0
O B:GLY122 2.3 17.4 1.0
O B:HOH1420 2.4 22.7 1.0
O B:HOH1014 2.4 23.0 1.0
O B:SER494 2.4 20.0 1.0
C B:SER494 3.2 17.7 1.0
C B:GLY124 3.4 16.6 1.0
C B:GLY122 3.4 16.6 1.0
CA B:ARG123 3.6 16.6 1.0
C B:ARG123 3.6 17.1 1.0
N B:GLY124 3.7 16.3 1.0
CA B:SER494 3.9 17.3 1.0
OD2 B:ASP427 4.0 24.2 1.0
N B:ARG123 4.0 16.5 1.0
O B:HOH1467 4.0 23.9 1.0
O B:HOH995 4.0 36.2 1.0
N B:ASP495 4.0 17.4 1.0
CB B:SER494 4.1 16.6 1.0
CA B:GLY124 4.1 16.3 1.0
CB B:ASP427 4.1 22.0 1.0
O B:ARG123 4.2 17.0 1.0
CA B:ASP495 4.4 18.3 1.0
N B:GLY125 4.5 17.2 1.0
CG B:ASP427 4.6 23.8 1.0
CB B:ASP495 4.6 18.6 1.0
CD1 B:TYR117 4.6 20.4 1.0
CL B:CL803 4.6 31.6 1.0
CA B:GLY122 4.7 16.5 1.0
OE2 B:GLU128 4.8 36.1 1.0
CE1 B:TYR117 4.8 20.1 1.0
CB B:ARG123 4.9 17.8 1.0
OG B:SER494 4.9 16.5 1.0
CA B:GLY125 4.9 16.3 1.0

Reference:

B.Wiseman, X.Carpena, M.Feliz, L.J.Donald, M.Pons, I.Fita, P.C.Loewen. Isonicotinic Acid Hydrazide Conversion to Isonicotinyl-Nad By Catalase-Peroxidases. J. Biol. Chem. V. 285 26662 2010.
ISSN: ESSN 1083-351X
PubMed: 20554537
DOI: 10.1074/JBC.M110.139428
Page generated: Mon Oct 7 23:57:42 2024

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