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Sodium in PDB 3x16: Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942

Enzymatic activity of Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942

All present enzymatic activity of Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942, PDB code: 3x16 was solved by T.Tada, K.Wada, S.Kamachi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.33 / 2.65
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.254, 108.254, 203.225, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25.4

Other elements in 3x16:

The structure of Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942 also contains other interesting chemical elements:

Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942 (pdb code 3x16). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942, PDB code: 3x16:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3x16

Go back to Sodium Binding Sites List in 3x16
Sodium binding site 1 out of 3 in the Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942


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 Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:38.1
occ:1.00
 O A:GLY105 2.3 35.7 1.0
O A:GLY107 2.3 37.9 1.0
O A:SER476 2.3 37.3 1.0
O A:HOH922 2.3 45.1 1.0
O A:HOH1045 2.4 41.9 1.0
C A:SER476 3.3 36.1 1.0
C A:GLY107 3.4 39.5 1.0
C A:GLY105 3.4 38.0 1.0
C A:ARG106 3.5 37.0 1.0
O A:HOH1010 3.5 38.4 1.0
N A:GLY107 3.5 39.7 1.0
CA A:ARG106 3.6 38.2 1.0
OD2 A:ASP413 4.0 37.2 1.0
CA A:SER476 4.0 38.6 1.0
N A:ARG106 4.0 37.0 1.0
CB A:ASP413 4.0 46.0 1.0
CB A:SER476 4.0 37.7 1.0
CA A:GLY107 4.1 37.3 1.0
O A:ARG106 4.1 37.1 1.0
N A:ASP477 4.2 39.3 1.0
N A:GLY108 4.4 39.9 1.0
CD1 A:TYR100 4.5 45.1 1.0
CG A:ASP413 4.5 43.4 1.0
CA A:GLY108 4.5 33.7 1.0
CA A:ASP477 4.5 43.3 1.0
CB A:ASP477 4.6 43.8 1.0
CA A:GLY105 4.7 36.9 1.0
CE1 A:TYR100 4.8 45.8 1.0
CB A:ARG106 5.0 36.6 1.0
OG A:SER476 5.0 36.1 1.0

Sodium binding site 2 out of 3 in 3x16

Go back to Sodium Binding Sites List in 3x16
Sodium binding site 2 out of 3 in the Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942


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 Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na803

b:40.0
occ:1.00
 O A:THR264 2.3 36.2 1.0
O A:HIS317 2.3 40.6 1.0
OD2 A:ASP322 2.3 45.9 1.0
O A:GLN320 2.3 47.8 1.0
OG1 A:THR315 2.4 32.1 1.0
OD1 A:ASP322 2.4 39.1 1.0
CG A:ASP322 2.7 41.7 1.0
C A:HIS317 3.3 41.9 1.0
CB A:THR315 3.4 35.0 1.0
C A:THR264 3.5 34.9 1.0
C A:GLN320 3.5 41.1 1.0
O A:HOH939 3.6 46.4 1.0
CG2 A:THR264 3.9 32.0 1.0
CG2 A:THR315 3.9 36.6 1.0
CB A:ASP322 4.1 38.2 1.0
N A:PRO318 4.2 37.1 1.0
CA A:PRO318 4.2 38.4 1.0
CA A:HIS317 4.3 41.7 1.0
N A:GLN320 4.4 37.0 1.0
CA A:THR264 4.4 35.5 1.0
CA A:GLN320 4.4 40.0 1.0
N A:VAL265 4.4 34.5 1.0
CB A:HIS317 4.5 42.0 1.0
N A:HIS317 4.5 44.2 1.0
CA A:VAL265 4.5 35.9 1.0
N A:ASP322 4.5 35.5 1.0
N A:TRP321 4.6 35.9 1.0
CG1 A:VAL265 4.6 38.6 1.0
C A:PRO318 4.7 35.8 1.0
C A:TRP321 4.7 35.5 1.0
CA A:TRP321 4.8 37.9 1.0
CB A:THR264 4.8 32.6 1.0
O A:HOH903 4.8 21.2 1.0
CA A:THR315 4.8 36.9 1.0
CA A:ASP322 4.8 36.6 1.0
CG A:GLN320 4.9 58.3 1.0
O A:HOH916 5.0 40.9 1.0

Sodium binding site 3 out of 3 in 3x16

Go back to Sodium Binding Sites List in 3x16
Sodium binding site 3 out of 3 in the Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na804

b:49.3
occ:1.00
 O A:GLU354 2.4 53.0 1.0
O A:HOH1046 2.4 59.1 1.0
O A:HOH1032 2.6 36.7 1.0
C A:GLU354 3.4 58.9 1.0
CA A:GLU354 3.9 62.8 1.0
O A:LEU356 4.0 45.4 1.0
O A:GLU353 4.5 57.4 1.0
CE1 A:HIS317 4.6 46.2 1.0
N A:ASP355 4.6 47.6 1.0
N A:LEU356 4.7 43.5 1.0
CB A:GLU354 4.7 65.3 1.0
C A:LEU356 5.0 42.3 1.0

Reference:

S.Kamachi, K.Hirabayashi, M.Tamoi, S.Shigeoka, T.Tada, K.Wada. Crystal Structure of the Catalase-Peroxidase Katg W78F Mutant From Synechococcus Elongatus PCC7942 in Complex with the Antitubercular Pro-Drug Isoniazid. Febs Lett. 2014.
ISSN: ISSN 0014-5793
PubMed: 25479089
DOI: 10.1016/J.FEBSLET.2014.11.037
Page generated: Mon Oct 7 14:03:36 2024

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