Sodium in PDB 8u3p: 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes

Protein crystallography data

The structure of 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes, PDB code: 8u3p was solved by A.Liu, J.Li, D.Ran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.55 / 1.79
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 150.58, 150.58, 311.542, 90, 90, 90
R / Rfree (%) 17.9 / 22

Other elements in 8u3p:

The structure of 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes (pdb code 8u3p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes, PDB code: 8u3p:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8u3p

Go back to Sodium Binding Sites List in 8u3p
Sodium binding site 1 out of 4 in the 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1001

b:18.6
occ:1.00
 O A:THR324 2.2 18.2 1.0
O A:THR271 2.4 16.1 1.0
O A:LYS327 2.5 16.9 1.0
O A:HOH1104 2.5 22.8 1.0
OG1 A:THR324 2.7 22.5 1.0
OG1 A:THR322 3.0 20.5 1.0
C A:THR324 3.2 20.3 1.0
C A:THR271 3.5 17.2 1.0
CG2 A:THR271 3.5 15.3 1.0
CB A:THR324 3.6 23.8 1.0
C A:LYS327 3.7 16.5 1.0
CB A:THR322 3.8 18.1 1.0
OD1 A:ASP329 3.9 21.5 1.0
CA A:THR324 3.9 20.8 1.0
CG2 A:THR322 4.1 16.9 1.0
N A:LYS327 4.2 20.4 1.0
N A:PRO325 4.2 19.4 1.0
CA A:THR271 4.2 17.3 1.0
N A:THR324 4.3 19.1 1.0
CA A:PRO325 4.4 21.2 1.0
CG A:ASP329 4.4 21.6 1.0
CA A:LYS327 4.4 17.5 1.0
OD2 A:ASP329 4.5 27.3 1.0
CB A:THR271 4.5 15.8 1.0
N A:PHE272 4.6 13.3 1.0
C A:PRO325 4.6 16.6 1.0
N A:ASP329 4.6 19.9 1.0
N A:TRP328 4.7 15.5 1.0
O A:HOH1178 4.8 16.9 1.0
CB A:LYS327 4.8 20.4 1.0
CA A:PHE272 4.9 15.3 1.0
CA A:TRP328 4.9 16.8 1.0
N A:THR326 4.9 18.2 1.0
O A:HOH1509 5.0 15.6 1.0
CG2 A:THR324 5.0 26.1 1.0

Sodium binding site 2 out of 4 in 8u3p

Go back to Sodium Binding Sites List in 8u3p
Sodium binding site 2 out of 4 in the 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1001

b:20.4
occ:1.00
 O B:THR324 2.2 18.9 1.0
O B:HOH1149 2.3 24.6 1.0
O B:LYS327 2.5 18.9 1.0
O B:THR271 2.5 16.7 1.0
OG1 B:THR324 2.8 26.3 1.0
OG1 B:THR322 2.9 20.0 1.0
C B:THR324 3.2 21.9 1.0
C B:THR271 3.6 15.5 1.0
CG2 B:THR271 3.6 19.5 1.0
C B:LYS327 3.7 19.6 1.0
CB B:THR324 3.7 24.4 1.0
CB B:THR322 3.7 21.6 1.0
CA B:THR324 3.9 23.1 1.0
OD1 B:ASP329 4.0 23.4 1.0
CG2 B:THR322 4.0 22.4 1.0
N B:PRO325 4.1 17.9 1.0
N B:LYS327 4.1 20.8 1.0
N B:THR324 4.2 22.1 1.0
CA B:PRO325 4.2 17.7 1.0
CA B:THR271 4.3 16.5 1.0
OD2 B:ASP329 4.3 28.7 1.0
CG B:ASP329 4.4 24.2 1.0
CA B:LYS327 4.4 19.3 1.0
C B:PRO325 4.5 20.7 1.0
CB B:THR271 4.5 17.1 1.0
N B:PHE272 4.6 16.8 1.0
N B:TRP328 4.7 18.9 1.0
N B:ASP329 4.7 19.2 1.0
O B:HOH1426 4.8 22.7 1.0
N B:THR326 4.8 19.3 1.0
CA B:PHE272 4.9 15.8 1.0
O B:PRO325 4.9 18.5 1.0
CA B:TRP328 4.9 19.1 1.0
CB B:LYS327 4.9 28.4 1.0
O B:HOH1270 5.0 19.4 1.0

Sodium binding site 3 out of 4 in 8u3p

Go back to Sodium Binding Sites List in 8u3p
Sodium binding site 3 out of 4 in the 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1001

b:18.1
occ:1.00
 O C:THR324 2.3 17.9 1.0
O C:THR271 2.3 16.4 1.0
O C:LYS327 2.4 21.5 1.0
O C:HOH2518 2.5 29.9 1.0
OG1 C:THR322 2.9 18.8 1.0
OG1 C:THR324 3.0 25.5 1.0
C C:THR324 3.2 19.3 1.0
CG2 C:THR271 3.4 16.5 1.0
C C:THR271 3.4 16.9 1.0
C C:LYS327 3.6 20.0 1.0
CB C:THR322 3.8 18.7 1.0
CB C:THR324 3.8 22.9 1.0
OD1 C:ASP329 3.9 24.0 1.0
CA C:THR324 4.0 20.8 1.0
CG2 C:THR322 4.0 17.3 1.0
CA C:THR271 4.1 15.6 1.0
N C:LYS327 4.1 20.3 1.0
N C:PRO325 4.2 18.7 1.0
CA C:PRO325 4.3 19.4 1.0
CB C:THR271 4.3 15.1 1.0
N C:THR324 4.4 18.6 1.0
CA C:LYS327 4.4 21.0 1.0
CG C:ASP329 4.4 29.5 1.0
N C:PHE272 4.5 13.2 1.0
OD2 C:ASP329 4.5 33.2 1.0
C C:PRO325 4.5 18.7 1.0
N C:TRP328 4.6 18.3 1.0
N C:ASP329 4.8 16.5 1.0
CA C:PHE272 4.8 16.4 1.0
CA C:TRP328 4.8 18.4 1.0
CB C:LYS327 4.9 22.0 1.0
O C:HOH2803 4.9 18.0 1.0
N C:THR326 4.9 19.4 1.0
O C:PRO325 4.9 15.1 1.0

Sodium binding site 4 out of 4 in 8u3p

Go back to Sodium Binding Sites List in 8u3p
Sodium binding site 4 out of 4 in the 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1001

b:18.9
occ:1.00
 O D:THR324 2.3 18.5 1.0
O D:THR271 2.3 15.9 1.0
O D:HOH1132 2.4 27.7 1.0
O D:LYS327 2.4 21.3 1.0
OG1 D:THR324 2.7 22.9 1.0
OG1 D:THR322 2.9 17.7 1.0
C D:THR324 3.2 19.8 1.0
C D:THR271 3.5 17.4 1.0
CG2 D:THR271 3.5 20.1 1.0
CB D:THR324 3.6 21.9 1.0
C D:LYS327 3.7 20.4 1.0
CB D:THR322 3.7 23.8 1.0
CA D:THR324 3.9 21.6 1.0
CG2 D:THR322 4.0 21.1 1.0
OD1 D:ASP329 4.0 22.4 1.0
N D:PRO325 4.1 16.2 1.0
CA D:THR271 4.2 16.5 1.0
N D:LYS327 4.2 18.2 1.0
CA D:PRO325 4.2 17.9 1.0
N D:THR324 4.3 23.1 1.0
CB D:THR271 4.4 13.6 1.0
CA D:LYS327 4.4 19.7 1.0
OD2 D:ASP329 4.5 28.9 1.0
CG D:ASP329 4.5 24.9 1.0
C D:PRO325 4.5 16.7 1.0
N D:PHE272 4.5 13.5 1.0
N D:TRP328 4.7 16.8 1.0
N D:ASP329 4.7 19.8 1.0
CA D:PHE272 4.8 15.8 1.0
O D:HOH1431 4.8 13.3 1.0
N D:THR326 4.9 18.3 1.0
CA D:TRP328 4.9 16.8 1.0
O D:PRO325 4.9 16.8 1.0
CB D:LYS327 4.9 19.1 1.0
CB D:SER331 4.9 23.2 1.0
CG2 D:THR324 5.0 25.7 1.0

Reference:

A.Liu, J.Li, D.Ran. 1.79 Angstrom Resolution Crystal Structure of Katg From Mycobacterium Tuberculosis with An Myw Cofactor After Heat Incubation For 60 Minutes To Be Published.
Page generated: Wed Oct 9 13:49:42 2024

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