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Sodium in PDB 3wxo: Crystal Structure of Isoniazid Bound Katg Catalase Peroxidase From Synechococcus Elongatus PCC7942

Enzymatic activity of Crystal Structure of Isoniazid Bound Katg Catalase Peroxidase From Synechococcus Elongatus PCC7942

All present enzymatic activity of Crystal Structure of Isoniazid Bound Katg Catalase Peroxidase From Synechococcus Elongatus PCC7942:
1.11.1.21;

Protein crystallography data

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

Resolution Low / High (Å) 35.09 / 2.12
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.654, 108.654, 202.891, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.7

Other elements in 3wxo:

The structure of Crystal Structure of Isoniazid Bound Katg Catalase Peroxidase 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 Isoniazid Bound Katg Catalase Peroxidase From Synechococcus Elongatus PCC7942 (pdb code 3wxo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Isoniazid Bound Katg Catalase Peroxidase From Synechococcus Elongatus PCC7942, PDB code: 3wxo:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3wxo

Go back to Sodium Binding Sites List in 3wxo
Sodium binding site 1 out of 4 in the Crystal Structure of Isoniazid Bound Katg Catalase Peroxidase 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 Isoniazid Bound Katg Catalase Peroxidase From Synechococcus Elongatus PCC7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na805

b:28.5
occ:1.00
 O A:SER476 2.3 28.0 1.0
O A:HOH955 2.3 24.8 1.0
O A:GLY107 2.3 26.0 1.0
O A:GLY105 2.4 25.1 1.0
O A:HOH1031 2.6 29.9 1.0
C A:SER476 3.2 26.8 1.0
C A:GLY107 3.5 26.4 1.0
N A:GLY107 3.5 25.1 1.0
C A:GLY105 3.5 28.0 1.0
C A:ARG106 3.6 27.2 1.0
CA A:ARG106 3.6 24.2 1.0
O A:HOH1371 3.7 36.0 1.0
O A:HOH1208 3.9 37.7 1.0
CA A:SER476 3.9 27.7 1.0
OD2 A:ASP413 3.9 31.9 1.0
CB A:ASP413 3.9 32.1 1.0
CB A:SER476 4.0 25.2 1.0
N A:ARG106 4.0 28.3 1.0
CA A:GLY107 4.1 25.8 1.0
N A:ASP477 4.1 31.6 1.0
O A:ARG106 4.3 25.2 1.0
CG A:ASP413 4.4 29.8 1.0
CA A:ASP477 4.5 31.7 1.0
CD1 A:TYR100 4.5 27.1 1.0
N A:GLY108 4.6 26.2 1.0
CB A:ASP477 4.6 31.5 1.0
CA A:GLY105 4.7 27.3 1.0
CE1 A:TYR100 4.8 27.9 1.0
CA A:GLY108 4.9 26.5 1.0
OG A:SER476 4.9 26.0 1.0
CB A:ARG106 5.0 26.6 1.0
O A:HOH919 5.0 28.8 1.0

Sodium binding site 2 out of 4 in 3wxo

Go back to Sodium Binding Sites List in 3wxo
Sodium binding site 2 out of 4 in the Crystal Structure of Isoniazid Bound Katg Catalase Peroxidase 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 Isoniazid Bound Katg Catalase Peroxidase From Synechococcus Elongatus PCC7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na806

b:29.2
occ:1.00
 O A:HIS317 2.3 26.8 1.0
O A:THR264 2.4 26.4 1.0
O A:GLN320 2.4 27.7 1.0
OD2 A:ASP322 2.6 32.7 1.0
OG1 A:THR315 2.8 26.4 1.0
OD1 A:ASP322 2.9 27.4 1.0
CG A:ASP322 3.0 30.8 1.0
C A:HIS317 3.4 30.3 1.0
C A:GLN320 3.6 30.0 1.0
C A:THR264 3.6 24.7 1.0
CB A:THR315 3.6 27.8 1.0
O A:HOH971 3.9 33.9 1.0
CG2 A:THR264 3.9 24.4 1.0
CG2 A:THR315 3.9 30.7 1.0
CA A:PRO318 4.0 27.9 1.0
N A:PRO318 4.1 29.6 1.0
N A:GLN320 4.2 30.9 1.0
CA A:HIS317 4.3 28.6 1.0
CA A:GLN320 4.3 31.8 1.0
CB A:ASP322 4.3 28.3 1.0
CA A:THR264 4.4 24.9 1.0
CB A:HIS317 4.4 32.2 1.0
C A:PRO318 4.5 27.1 1.0
N A:ASP322 4.5 31.1 1.0
N A:HIS317 4.5 29.6 1.0
N A:VAL265 4.5 26.2 1.0
N A:TRP321 4.6 27.9 1.0
CG1 A:VAL265 4.6 33.7 1.0
CA A:VAL265 4.6 26.5 1.0
CG A:GLN320 4.7 45.0 1.0
C A:TRP321 4.7 28.1 1.0
O A:HOH911 4.8 25.1 1.0
CB A:THR264 4.8 26.3 1.0
CA A:TRP321 4.8 29.2 1.0
N A:THR319 4.9 32.2 1.0
O A:PRO318 4.9 30.4 1.0
O A:HOH1020 4.9 37.1 1.0
CA A:ASP322 5.0 29.8 1.0

Sodium binding site 3 out of 4 in 3wxo

Go back to Sodium Binding Sites List in 3wxo
Sodium binding site 3 out of 4 in the Crystal Structure of Isoniazid Bound Katg Catalase Peroxidase 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 Isoniazid Bound Katg Catalase Peroxidase From Synechococcus Elongatus PCC7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na807

b:47.6
occ:1.00
 O A:ASN43 2.3 29.4 1.0
O A:ARG40 2.4 24.6 1.0
O A:HOH953 2.5 40.6 1.0
O A:HOH1024 3.1 45.1 1.0
C A:ASN43 3.5 25.5 1.0
C A:ARG40 3.6 27.8 1.0
O A:MET45 4.1 37.1 1.0
N A:ASN43 4.2 27.9 1.0
CA A:ARG40 4.2 27.8 1.0
CA A:ASN43 4.2 28.0 1.0
CB A:ASN43 4.2 32.5 1.0
CA A:PRO44 4.4 27.7 1.0
N A:PRO44 4.5 26.9 1.0
CB A:ARG40 4.5 34.3 1.0
N A:LYS41 4.6 25.7 1.0
O A:HOH1363 4.6 60.7 1.0
CA A:LYS41 4.6 27.2 1.0
C A:PRO44 4.7 28.5 1.0
C A:LYS41 4.8 26.0 1.0
N A:MET45 4.9 29.1 1.0

Sodium binding site 4 out of 4 in 3wxo

Go back to Sodium Binding Sites List in 3wxo
Sodium binding site 4 out of 4 in the Crystal Structure of Isoniazid Bound Katg Catalase Peroxidase From Synechococcus Elongatus PCC7942


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Isoniazid Bound Katg Catalase Peroxidase From Synechococcus Elongatus PCC7942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na808

b:34.1
occ:1.00
 O A:HOH1176 2.4 33.8 1.0
O A:HOH1015 2.4 31.2 1.0
O A:ASP695 2.4 31.2 1.0
OD1 A:ASN696 2.5 29.8 1.0
C A:ASP695 3.5 31.3 1.0
CG A:ASN696 3.7 29.5 1.0
O A:HOH1323 3.9 43.7 1.0
CA A:ASN696 3.9 29.4 1.0
O A:HOH1087 4.1 47.4 1.0
N A:ASN696 4.2 31.9 1.0
CG A:ASP695 4.2 33.3 1.0
O A:HOH1175 4.3 37.8 1.0
OD2 A:ASP695 4.3 31.8 1.0
CB A:LYS699 4.4 35.7 1.0
CB A:ASP695 4.4 34.3 1.0
CB A:ASN696 4.4 28.0 1.0
CA A:ASP695 4.6 31.8 1.0
OD1 A:ASP695 4.6 33.6 1.0
ND2 A:ASN696 4.7 26.3 1.0
N A:LYS699 5.0 31.6 1.0
C A:ASN696 5.0 31.2 1.0
CD A:LYS699 5.0 38.4 1.0

Reference:

S.Kamachi, K.Hirabayashi, M.Tamoi, S.Shigeoka, T.Tada, K.Wada. The Crystal Structure of Isoniazid-Bound Katg Catalase-Peroxidase From Synechococcus Elongatus PCC7942. Febs J. V. 282 54 2015.
ISSN: ISSN 1742-464X
PubMed: 25303560
DOI: 10.1111/FEBS.13102
Page generated: Mon Oct 7 14:01:57 2024

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