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Sodium in PDB 8w1w: 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor

Enzymatic activity of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor

All present enzymatic activity of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor:
1.11.1.21;

Protein crystallography data

The structure of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor, PDB code: 8w1w was solved by A.Liu, J.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.99 / 2.03
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 150.674, 150.674, 311.112, 90, 90, 90
R / Rfree (%) 16.6 / 22.3

Other elements in 8w1w:

The structure of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor (pdb code 8w1w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor, PDB code: 8w1w:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8w1w

Go back to Sodium Binding Sites List in 8w1w
Sodium binding site 1 out of 4 in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:16.4
occ:1.00
 O A:HOH941 2.2 21.7 1.0
O A:THR324 2.3 15.0 1.0
O A:THR271 2.4 13.0 1.0
O A:LYS327 2.5 13.8 1.0
OG1 A:THR324 2.8 20.1 1.0
OG1 A:THR322 3.0 11.1 1.0
C A:THR324 3.3 18.8 1.0
C A:THR271 3.5 11.1 1.0
CG2 A:THR271 3.6 11.3 1.0
C A:LYS327 3.7 14.4 1.0
CB A:THR322 3.7 18.5 1.0
CB A:THR324 3.8 18.1 1.0
CG2 A:THR322 3.9 16.9 1.0
OD1 A:ASP329 3.9 21.3 1.0
CA A:THR324 4.0 15.9 1.0
CA A:THR271 4.2 12.8 1.0
N A:PRO325 4.2 13.7 1.0
N A:LYS327 4.2 15.6 1.0
CA A:PRO325 4.3 14.9 1.0
N A:THR324 4.3 20.1 1.0
CG A:ASP329 4.4 21.4 1.0
CA A:LYS327 4.4 16.7 1.0
CB A:THR271 4.5 11.9 1.0
OD2 A:ASP329 4.5 24.3 1.0
C A:PRO325 4.6 14.4 1.0
N A:PHE272 4.6 13.5 1.0
N A:ASP329 4.6 16.9 1.0
N A:TRP328 4.7 15.7 1.0
CA A:TRP328 4.8 15.2 1.0
CB A:LYS327 4.9 20.6 1.0
O A:PRO325 4.9 14.0 1.0
O A:HOH1209 4.9 13.2 1.0
CA A:PHE272 4.9 11.1 1.0
O A:HOH960 4.9 14.9 1.0
N A:THR326 4.9 15.1 1.0

Sodium binding site 2 out of 4 in 8w1w

Go back to Sodium Binding Sites List in 8w1w
Sodium binding site 2 out of 4 in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:15.6
occ:1.00
 O B:THR324 2.1 15.0 1.0
O B:THR271 2.4 12.9 1.0
O B:LYS327 2.5 13.3 1.0
O B:HOH976 2.6 17.9 1.0
OG1 B:THR324 2.7 20.4 1.0
OG1 B:THR322 2.9 14.9 1.0
C B:THR324 3.2 17.1 1.0
C B:THR271 3.5 12.8 1.0
CB B:THR322 3.6 14.4 1.0
CG2 B:THR271 3.6 10.8 1.0
CB B:THR324 3.7 20.9 1.0
C B:LYS327 3.7 12.4 1.0
CA B:THR324 3.9 18.9 1.0
CG2 B:THR322 3.9 11.8 1.0
N B:PRO325 4.1 16.5 1.0
CA B:THR271 4.1 11.1 1.0
OD1 B:ASP329 4.2 18.1 1.0
N B:LYS327 4.2 15.6 1.0
N B:THR324 4.2 16.8 1.0
CA B:PRO325 4.3 15.9 1.0
OD2 B:ASP329 4.4 23.0 1.0
CB B:THR271 4.4 11.3 1.0
CA B:LYS327 4.5 15.9 1.0
C B:PRO325 4.5 12.8 1.0
CG B:ASP329 4.5 18.8 1.0
N B:PHE272 4.6 12.6 1.0
N B:TRP328 4.7 13.0 1.0
O B:HOH1235 4.7 11.9 1.0
N B:ASP329 4.8 14.0 1.0
CA B:PHE272 4.8 12.6 1.0
CB B:LYS327 4.9 17.7 1.0
O B:PRO325 4.9 12.7 1.0
N B:THR326 4.9 15.9 1.0
O B:HOH926 4.9 13.7 1.0
CA B:TRP328 4.9 12.8 1.0

Sodium binding site 3 out of 4 in 8w1w

Go back to Sodium Binding Sites List in 8w1w
Sodium binding site 3 out of 4 in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na802

b:19.6
occ:1.00
 O C:THR324 2.1 14.1 1.0
O C:THR271 2.3 13.8 1.0
O C:HOH935 2.3 19.3 1.0
O C:LYS327 2.6 13.3 1.0
OG1 C:THR322 2.8 14.1 1.0
OG1 C:THR324 2.8 17.1 1.0
C C:THR324 3.1 12.5 1.0
C C:THR271 3.5 11.9 1.0
CB C:THR322 3.6 14.6 1.0
CG2 C:THR271 3.6 12.4 1.0
CB C:THR324 3.7 17.9 1.0
C C:LYS327 3.7 11.8 1.0
CA C:THR324 3.9 15.3 1.0
CG2 C:THR322 3.9 14.0 1.0
N C:PRO325 3.9 13.1 1.0
CA C:PRO325 4.0 13.6 1.0
N C:LYS327 4.1 14.2 1.0
OD1 C:ASP329 4.2 21.6 1.0
CA C:THR271 4.2 10.1 1.0
N C:THR324 4.3 15.1 1.0
C C:PRO325 4.4 13.2 1.0
CA C:LYS327 4.4 12.9 1.0
OD2 C:ASP329 4.4 22.2 1.0
N C:PHE272 4.5 10.9 1.0
CB C:THR271 4.6 10.4 1.0
CG C:ASP329 4.6 17.4 1.0
O C:HOH1278 4.7 11.5 1.0
CA C:PHE272 4.7 11.4 1.0
N C:TRP328 4.8 12.7 1.0
N C:THR326 4.8 12.2 1.0
O C:PRO325 4.8 14.0 1.0
CB C:LYS327 4.8 13.8 1.0
N C:ASP329 5.0 15.4 1.0

Sodium binding site 4 out of 4 in 8w1w

Go back to Sodium Binding Sites List in 8w1w
Sodium binding site 4 out of 4 in the 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.03 Angstrom Resolution Crystal Structure of As-Isolated Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na802

b:15.4
occ:1.00
 O D:THR324 2.2 13.0 1.0
O D:THR271 2.4 11.8 1.0
O D:LYS327 2.6 14.2 1.0
OG1 D:THR322 2.9 15.1 1.0
OG1 D:THR324 2.9 18.5 1.0
C D:THR324 3.2 13.5 1.0
C D:THR271 3.6 11.6 1.0
CB D:THR322 3.6 12.4 1.0
CG2 D:THR271 3.6 14.4 1.0
CB D:THR324 3.7 16.8 1.0
C D:LYS327 3.7 12.9 1.0
CG2 D:THR322 3.9 15.2 1.0
CA D:THR324 3.9 14.2 1.0
OD1 D:ASP329 3.9 21.6 1.0
N D:PRO325 4.1 15.8 1.0
CA D:THR271 4.2 12.7 1.0
CA D:PRO325 4.2 13.4 1.0
N D:LYS327 4.3 15.0 1.0
N D:THR324 4.3 17.4 1.0
CA D:LYS327 4.5 13.8 1.0
CG D:ASP329 4.5 20.7 1.0
OD2 D:ASP329 4.5 24.2 1.0
CB D:THR271 4.5 10.6 1.0
C D:PRO325 4.5 15.9 1.0
N D:PHE272 4.6 8.7 1.0
N D:TRP328 4.7 12.0 1.0
CB D:LYS327 4.8 14.7 1.0
CA D:PHE272 4.8 9.5 1.0
O D:HOH1280 4.8 12.4 1.0
N D:ASP329 4.9 16.0 1.0
CA D:TRP328 4.9 11.5 1.0
O D:PRO325 4.9 13.4 1.0
CB D:SER331 5.0 16.9 1.0

Reference:

J.Li, R.Duan, E.S.Traore, R.C.Nguyen, I.Davis, W.P.Griffth, D.C.Goodwin, A.A.Jarzecki, A.Liu. Indole-N-Linked Hydroperoxyl Adduct of Protein-Derived Cofactor Modulating Catalase-Peroxidase Functions. Angew.Chem.Int.Ed.Engl. 07018 2024.
ISSN: ESSN 1521-3773
PubMed: 39300819
DOI: 10.1002/ANIE.202407018
Page generated: Mon Aug 18 16:13:43 2025

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