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Sodium in PDB 8dwr: Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis, PDB code: 8dwr was solved by A.Diaz-Vilchis, B.Uribe-Vazquez, A.Avila-Linares, E.Rudino-Pinera, X.Soberon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.671, 150.817, 127.037, 90, 90.45, 90
R / Rfree (%) 18.1 / 22.7

Other elements in 8dwr:

The structure of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis (pdb code 8dwr). 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 the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis, PDB code: 8dwr:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8dwr

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Sodium binding site 1 out of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis


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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na803

b:19.4
occ:1.00
 O A:HOH1028 2.5 17.3 1.0
O A:GLY120 2.5 17.2 1.0
O A:SER486 2.5 14.9 1.0
O A:HOH1417 2.5 26.2 1.0
O A:GLY118 2.6 13.1 1.0
C A:SER486 3.2 16.9 1.0
CA A:ARG119 3.5 12.5 1.0
C A:ARG119 3.5 15.3 1.0
N A:GLY120 3.6 16.6 1.0
C A:GLY120 3.6 16.5 1.0
C A:GLY118 3.6 15.8 1.0
CA A:SER486 3.9 18.1 1.0
N A:ASP487 4.0 17.7 1.0
CB A:SER486 4.0 13.1 1.0
N A:ARG119 4.1 13.1 1.0
O A:HOH1094 4.1 18.4 1.0
O A:HOH1397 4.1 24.2 1.0
OD2 A:ASP419 4.1 16.7 1.0
O A:HOH1438 4.2 17.0 1.0
CA A:GLY120 4.2 15.5 1.0
O A:ARG119 4.2 14.6 1.0
CA A:ASP487 4.3 14.8 1.0
CB A:ASP419 4.3 16.3 1.0
O A:HOH1205 4.4 28.7 1.0
CB A:ASP487 4.5 13.2 1.0
O A:HOH915 4.6 29.6 1.0
CD1 A:TYR113 4.7 13.5 1.0
N A:GLY121 4.7 15.1 1.0
CG A:ASP419 4.7 18.8 1.0
CB A:ARG119 4.7 13.0 1.0
CA A:GLY118 4.9 13.5 1.0
OG A:SER486 4.9 15.8 1.0

Sodium binding site 2 out of 4 in 8dwr

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Sodium binding site 2 out of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis


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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na803

b:19.7
occ:1.00
 O B:HOH1382 2.3 19.4 1.0
O B:GLY120 2.4 15.8 1.0
O B:GLY118 2.5 14.3 1.0
O B:SER486 2.5 15.7 1.0
O B:HOH920 2.6 16.5 1.0
C B:SER486 3.3 14.9 1.0
N B:GLY120 3.5 12.6 1.0
CA B:ARG119 3.5 13.9 1.0
C B:GLY120 3.5 13.4 1.0
C B:ARG119 3.6 15.6 1.0
C B:GLY118 3.6 15.5 1.0
CA B:SER486 4.0 16.6 1.0
N B:ARG119 4.0 15.2 1.0
N B:ASP487 4.1 16.6 1.0
CA B:GLY120 4.1 12.4 1.0
CB B:SER486 4.1 14.5 1.0
O B:HOH1413 4.1 15.7 1.0
OD2 B:ASP419 4.2 17.6 1.0
O B:HOH997 4.3 20.9 1.0
O B:ARG119 4.3 13.8 1.0
CB B:ASP419 4.3 16.9 1.0
CA B:ASP487 4.4 14.1 1.0
CB B:ASP487 4.6 15.4 1.0
N B:GLY121 4.7 17.8 1.0
CD1 B:TYR113 4.7 14.6 1.0
CB B:ARG119 4.7 15.0 1.0
CG B:ASP419 4.8 21.5 1.0
CA B:GLY118 4.9 14.6 1.0
O B:HOH1120 5.0 29.5 1.0

Sodium binding site 3 out of 4 in 8dwr

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Sodium binding site 3 out of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis


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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na803

b:23.9
occ:1.00
 O C:HOH1332 2.4 21.2 1.0
O C:GLY118 2.4 15.2 1.0
O C:GLY120 2.5 19.5 1.0
O C:SER486 2.6 24.4 1.0
O C:HOH961 2.6 19.1 1.0
C C:SER486 3.2 22.7 1.0
CA C:ARG119 3.4 20.1 1.0
C C:GLY118 3.5 18.1 1.0
C C:ARG119 3.5 16.6 1.0
N C:GLY120 3.5 17.5 1.0
C C:GLY120 3.6 15.9 1.0
N C:ARG119 3.9 15.6 1.0
CA C:SER486 3.9 17.4 1.0
N C:ASP487 3.9 18.0 1.0
CB C:SER486 4.0 16.7 1.0
O C:ARG119 4.1 15.8 1.0
OD2 C:ASP419 4.2 20.6 1.0
CA C:GLY120 4.2 15.3 1.0
O C:HOH1221 4.2 21.9 1.0
CA C:ASP487 4.3 18.4 1.0
CB C:ASP419 4.3 21.5 1.0
O C:HOH1355 4.4 18.3 1.0
CB C:ASP487 4.5 15.3 1.0
O C:HOH937 4.6 29.2 1.0
O C:HOH1270 4.6 32.0 1.0
CD1 C:TYR113 4.7 17.6 1.0
CB C:ARG119 4.7 16.7 1.0
N C:GLY121 4.7 15.6 1.0
CG C:ASP419 4.7 20.0 1.0
CA C:GLY118 4.8 16.3 1.0
OG C:SER486 4.9 15.8 1.0
CE1 C:TYR113 5.0 14.6 1.0

Sodium binding site 4 out of 4 in 8dwr

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Sodium binding site 4 out of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis


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 the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na802

b:26.5
occ:1.00
 O D:GLY120 2.4 22.2 1.0
O D:GLY118 2.5 21.2 1.0
O D:HOH1186 2.5 27.0 1.0
O D:HOH1322 2.6 23.4 1.0
O D:SER486 2.6 24.0 1.0
C D:SER486 3.3 19.1 1.0
CA D:ARG119 3.4 18.4 1.0
C D:ARG119 3.5 18.4 1.0
N D:GLY120 3.5 18.8 1.0
C D:GLY120 3.5 18.8 1.0
C D:GLY118 3.6 22.8 1.0
N D:ARG119 4.0 23.1 1.0
CA D:SER486 4.0 22.5 1.0
O D:HOH1175 4.0 25.2 1.0
CB D:SER486 4.1 23.9 1.0
O D:HOH1336 4.1 26.1 1.0
N D:ASP487 4.1 20.7 1.0
CA D:GLY120 4.1 20.2 1.0
O D:ARG119 4.2 17.8 1.0
O D:HOH1309 4.3 35.7 1.0
CB D:ASP419 4.4 21.7 1.0
OD2 D:ASP419 4.4 28.7 1.0
CA D:ASP487 4.4 23.4 1.0
N D:GLY121 4.6 19.4 1.0
CD1 D:TYR113 4.7 19.9 1.0
CB D:ARG119 4.7 23.0 1.0
CB D:ASP487 4.7 22.6 1.0
CA D:GLY118 4.9 21.6 1.0
CG D:ASP419 4.9 29.1 1.0
CA D:GLY121 4.9 19.1 1.0

Reference:

B.Uribe-Vazquez, A.Diaz-Vilchis, A.Avila-Linares, G.Saab-Rincon, Y.Marin-Tovar, H.Flores-Soto, N.Pastor-Colon, E.Rudino-Pinera, X.Soberon. Crystal Structure and Biochemical Characterization of the Mycobacterium Tuberculosis Katg-L333V From A Clinical Isolate To Be Published.
Page generated: Wed Oct 9 11:37:06 2024

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