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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy