Atomistry » Sodium » PDB 8dqm-8ekz » 8dwr
Atomistry »
  Sodium »
    PDB 8dqm-8ekz »
      8dwr »

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

Go back to Sodium Binding Sites List in 8dwr
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

Go back to Sodium Binding Sites List in 8dwr
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

Go back to Sodium Binding Sites List in 8dwr
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

Go back to Sodium Binding Sites List in 8dwr
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: Thu Dec 28 11:36:07 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy