Sodium in PDB 8w1y: 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute

Enzymatic activity of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute

All present enzymatic activity of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute:
1.11.1.21;

Protein crystallography data

The structure of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute, PDB code: 8w1y was solved by J.Li, R.Duan, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.93 / 2.30
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 150.511, 150.511, 155.225, 90, 90, 90
R / Rfree (%) 19.1 / 24.7

Other elements in 8w1y:

The structure of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute (pdb code 8w1y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute, PDB code: 8w1y:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8w1y

Go back to Sodium Binding Sites List in 8w1y
Sodium binding site 1 out of 4 in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:40.5
occ:1.00
 O A:THR324 2.5 31.1 1.0
O A:LYS327 2.7 26.7 1.0
OG1 A:THR324 2.8 39.7 1.0
OG1 A:THR322 3.0 26.1 1.0
O A:THR271 3.0 30.9 1.0
OD1 A:ASP329 3.1 35.2 1.0
C A:THR324 3.4 31.7 1.0
OD2 A:ASP329 3.4 41.6 1.0
CG A:ASP329 3.6 38.0 1.0
CG2 A:THR271 3.6 30.9 1.0
CB A:THR322 3.7 32.2 1.0
CB A:THR324 3.7 39.0 1.0
C A:LYS327 3.9 28.8 1.0
CG2 A:THR322 4.0 25.4 1.0
CA A:THR324 4.0 35.4 1.0
C A:THR271 4.1 27.4 1.0
N A:THR324 4.2 34.6 1.0
N A:PRO325 4.4 31.1 1.0
N A:LYS327 4.5 29.7 1.0
CA A:PRO325 4.6 32.4 1.0
CB A:SER331 4.6 30.5 1.0
N A:ASP329 4.6 33.2 1.0
CA A:THR271 4.6 26.0 1.0
CA A:LYS327 4.6 34.3 1.0
OG A:SER331 4.7 34.0 1.0
CB A:THR271 4.7 30.0 1.0
O A:HOH1003 4.7 28.2 1.0
CB A:LYS327 4.8 35.9 1.0
N A:TRP328 4.9 33.3 1.0
C A:PRO325 4.9 32.2 1.0
CB A:ASP329 4.9 31.0 1.0

Sodium binding site 2 out of 4 in 8w1y

Go back to Sodium Binding Sites List in 8w1y
Sodium binding site 2 out of 4 in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:43.3
occ:1.00
 OD1 B:ASP329 2.7 38.9 1.0
OG1 B:THR324 2.7 41.3 1.0
O B:LYS327 2.8 35.9 1.0
O B:THR324 3.0 32.4 1.0
OG1 B:THR322 3.0 35.5 1.0
O B:THR271 3.1 33.8 1.0
CG B:ASP329 3.3 34.5 1.0
OD2 B:ASP329 3.3 40.6 1.0
CG2 B:THR271 3.5 28.1 1.0
CB B:THR322 3.6 33.4 1.0
C B:THR324 3.8 32.9 1.0
CG2 B:THR322 3.9 28.9 1.0
CB B:THR324 4.0 33.0 1.0
C B:LYS327 4.0 33.6 1.0
CB B:SER331 4.1 29.5 1.0
C B:THR271 4.1 32.5 1.0
CA B:THR324 4.3 37.5 1.0
N B:ASP329 4.4 36.2 1.0
N B:THR324 4.4 33.8 1.0
CA B:THR271 4.5 29.4 1.0
OG B:SER331 4.5 37.1 1.0
CB B:THR271 4.5 28.4 1.0
CB B:ASP329 4.6 29.0 1.0
N B:PRO325 4.8 30.7 1.0
N B:LYS327 4.8 33.2 1.0
O B:ASP329 4.8 30.1 1.0
O B:HOH1003 4.8 27.2 1.0
C B:TRP328 4.9 34.5 1.0
CA B:LYS327 4.9 30.9 1.0
CA B:ASP329 4.9 34.9 1.0
CA B:TRP328 4.9 28.3 1.0
N B:SER331 4.9 23.9 1.0
CA B:PRO325 4.9 33.8 1.0
N B:TRP328 4.9 28.4 1.0
CG2 B:THR324 5.0 33.1 1.0

Sodium binding site 3 out of 4 in 8w1y

Go back to Sodium Binding Sites List in 8w1y
Sodium binding site 3 out of 4 in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na802

b:38.3
occ:1.00
 O C:THR324 2.4 28.9 1.0
O C:LYS327 2.7 28.5 1.0
O C:THR271 2.9 28.0 1.0
OG1 C:THR322 2.9 32.0 1.0
OG1 C:THR324 3.0 32.8 1.0
OD1 C:ASP329 3.2 35.0 1.0
C C:THR324 3.3 30.1 1.0
CG2 C:THR271 3.6 29.9 1.0
CB C:THR322 3.7 28.3 1.0
CG C:ASP329 3.8 36.5 1.0
CG2 C:THR322 3.8 29.0 1.0
CB C:THR324 3.8 34.6 1.0
OD2 C:ASP329 3.9 44.5 1.0
C C:LYS327 3.9 29.4 1.0
CA C:THR324 4.0 35.1 1.0
C C:THR271 4.0 26.1 1.0
N C:THR324 4.2 30.7 1.0
N C:PRO325 4.3 30.1 1.0
CA C:PRO325 4.5 33.3 1.0
N C:ASP329 4.5 33.7 1.0
N C:LYS327 4.5 29.1 1.0
CA C:THR271 4.5 26.8 1.0
OG C:SER331 4.6 39.3 1.0
CB C:SER331 4.7 28.1 1.0
CB C:THR271 4.7 31.0 1.0
C C:PRO325 4.7 33.1 1.0
CA C:LYS327 4.7 31.8 1.0
N C:TRP328 4.9 29.5 1.0
O C:HOH1001 4.9 27.6 1.0
C C:TRP328 5.0 33.0 1.0

Sodium binding site 4 out of 4 in 8w1y

Go back to Sodium Binding Sites List in 8w1y
Sodium binding site 4 out of 4 in the 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.30 Angstrom Resolution Intermediate Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw-Ooh Cofactor Soaked with Peroxide For 1 Minute within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na802

b:40.0
occ:1.00
 OG1 D:THR324 2.7 46.8 1.0
O D:LYS327 2.7 37.2 1.0
OD1 D:ASP329 2.8 37.3 1.0
O D:THR324 2.9 35.6 1.0
OG1 D:THR322 3.0 33.3 1.0
O D:THR271 3.0 33.4 1.0
CG2 D:THR271 3.4 25.5 1.0
CG D:ASP329 3.5 35.6 1.0
CB D:THR322 3.6 34.7 1.0
OD2 D:ASP329 3.7 42.0 1.0
C D:THR324 3.8 34.4 1.0
CG2 D:THR322 3.9 31.3 1.0
C D:LYS327 4.0 34.2 1.0
C D:THR271 4.1 29.1 1.0
CB D:THR324 4.1 38.9 1.0
CB D:SER331 4.4 27.6 1.0
CA D:THR324 4.4 36.1 1.0
N D:ASP329 4.4 37.8 1.0
CA D:THR271 4.4 28.2 1.0
CB D:THR271 4.5 26.6 1.0
N D:THR324 4.5 36.1 1.0
O D:HOH950 4.6 28.0 1.0
N D:LYS327 4.7 35.6 1.0
N D:PRO325 4.8 33.3 1.0
OG D:SER331 4.8 38.6 1.0
CA D:TRP328 4.8 29.3 1.0
O D:ASP329 4.8 32.7 1.0
C D:TRP328 4.8 34.2 1.0
N D:TRP328 4.8 29.1 1.0
CB D:ASP329 4.8 34.1 1.0
CA D:LYS327 4.9 35.0 1.0
CA D:PRO325 4.9 39.2 1.0
CG2 D:THR324 5.0 39.8 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: Thu Oct 31 23:01:27 2024

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