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Sodium in PDB 5sxs: Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound

Enzymatic activity of Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound

All present enzymatic activity of Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound, PDB code: 5sxs 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 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.436, 114.172, 174.232, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.3

Other elements in 5sxs:

The structure of Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp 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 Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound (pdb code 5sxs). 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 with Isonicotinic Acid Hydrazide and Amp Bound, PDB code: 5sxs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5sxs

Go back to Sodium Binding Sites List in 5sxs
Sodium binding site 1 out of 2 in the Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp 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 Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:16.7
occ:1.00
O A:GLY124 2.3 17.8 1.0
O A:SER494 2.3 16.3 1.0
O A:GLY122 2.4 18.0 1.0
O A:HOH1405 2.5 21.9 1.0
O A:HOH1155 2.5 22.5 1.0
C A:SER494 3.2 16.7 1.0
C A:GLY124 3.5 17.5 1.0
C A:GLY122 3.5 17.5 1.0
N A:GLY124 3.5 17.6 1.0
C A:ARG123 3.6 17.8 1.0
CA A:ARG123 3.6 18.7 1.0
CA A:SER494 4.0 17.1 1.0
O A:HOH1459 4.0 18.2 1.0
N A:ARG123 4.0 17.4 1.0
OD2 A:ASP427 4.0 18.4 1.0
O A:HOH1092 4.0 30.8 1.0
N A:ASP495 4.1 16.6 1.0
CA A:GLY124 4.1 18.3 1.0
CB A:ASP427 4.1 17.6 1.0
O A:ARG123 4.1 18.2 1.0
CB A:SER494 4.2 18.4 1.0
CA A:ASP495 4.4 16.8 1.0
N A:GLY125 4.6 17.8 1.0
CG A:ASP427 4.6 18.0 1.0
CB A:ASP495 4.6 16.9 1.0
CL A:CL803 4.6 25.7 0.8
CD1 A:TYR117 4.7 18.0 1.0
CA A:GLY122 4.8 17.4 1.0
CB A:ARG123 4.9 19.9 1.0
OE2 A:GLU128 4.9 25.0 1.0
CA A:GLY125 4.9 16.7 1.0
OG A:SER494 4.9 18.3 1.0
CE1 A:TYR117 5.0 18.3 1.0

Sodium binding site 2 out of 2 in 5sxs

Go back to Sodium Binding Sites List in 5sxs
Sodium binding site 2 out of 2 in the Crystal Structure of Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp 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 Catalase-Peroxidase Katg with Isonicotinic Acid Hydrazide and Amp 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 15.6 1.0
O B:SER494 2.3 18.1 1.0
O B:HOH1406 2.3 16.4 1.0
O B:HOH1153 2.5 17.0 1.0
C B:SER494 3.1 17.1 1.0
C B:GLY122 3.5 16.0 1.0
C B:GLY124 3.5 18.7 1.0
N B:GLY124 3.6 18.7 1.0
C B:ARG123 3.6 18.1 1.0
CA B:ARG123 3.6 17.0 1.0
CA B:SER494 3.9 17.1 1.0
N B:ASP495 4.0 17.5 1.0
OD2 B:ASP427 4.0 17.8 1.0
N B:ARG123 4.0 16.0 1.0
O B:HOH1523 4.0 20.4 1.0
CB B:ASP427 4.1 20.6 1.0
CB B:SER494 4.1 16.6 1.0
O B:HOH1092 4.2 27.1 1.0
O B:ARG123 4.2 17.0 1.0
CA B:GLY124 4.2 18.9 1.0
CA B:ASP495 4.4 17.5 1.0
CB B:ASP495 4.5 16.6 1.0
CG B:ASP427 4.6 19.9 1.0
N B:GLY125 4.6 17.6 1.0
CD1 B:TYR117 4.7 16.4 1.0
CL B:CL803 4.7 20.8 0.8
CA B:GLY122 4.8 16.1 1.0
OE2 B:GLU128 4.9 26.5 1.0
OG B:SER494 4.9 17.6 1.0
CA B:GLY125 4.9 17.0 1.0
CB B:ARG123 4.9 17.1 1.0
CE1 B:TYR117 4.9 15.9 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: Tue Dec 15 11:34:06 2020

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