Atomistry » Sodium » PDB 6tbt-6tos » 6tgh
Atomistry »
  Sodium »
    PDB 6tbt-6tos »
      6tgh »

Sodium in PDB 6tgh: Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex

Enzymatic activity of Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex

All present enzymatic activity of Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex:
2.1.2.1;

Protein crystallography data

The structure of Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex, PDB code: 6tgh was solved by G.Petrillo, K.Hernandez, J.Bujons, P.Clapes, I.Uson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.76 / 2.12
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 200.795, 112.930, 131.918, 90.00, 93.10, 90.00
R / Rfree (%) 23.7 / 28.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex (pdb code 6tgh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex, PDB code: 6tgh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6tgh

Go back to Sodium Binding Sites List in 6tgh
Sodium binding site 1 out of 3 in the Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:48.3
occ:1.00
 O A:ALA203 2.7 48.7 1.0
O A:HIS229 2.8 36.5 1.0
N A:LEU232 3.1 40.7 1.0
N A:THR231 3.2 43.3 1.0
CB A:LEU232 3.4 39.2 1.0
CB A:ALA206 3.4 38.4 1.0
CB A:LYS230 3.5 39.0 1.0
C A:HIS229 3.7 37.3 1.0
OG1 A:THR231 3.7 38.7 1.0
C A:LYS230 3.7 43.1 1.0
O A:THR227 3.8 42.6 1.0
C A:ALA203 3.8 40.7 1.0
CA A:LEU232 3.8 41.0 1.0
CA A:LYS230 3.9 41.7 1.0
OG1 A:THR227 4.0 32.8 1.0
C A:THR231 4.0 41.1 1.0
CA A:THR231 4.0 39.0 1.0
N A:ALA206 4.1 32.4 1.0
OG1 A:THR226 4.1 38.4 1.0
N A:LYS230 4.2 36.5 1.0
CA A:ALA206 4.2 33.9 1.0
N A:GLY207 4.2 34.8 1.0
CB A:THR231 4.5 40.4 1.0
CA A:ALA203 4.5 38.6 1.0
C A:THR227 4.6 37.5 1.0
O A:LYS230 4.6 46.5 1.0
C A:ALA206 4.6 28.2 1.0
CG A:LYS230 4.7 38.5 1.0
CG A:LEU232 4.7 41.2 1.0
O A:THR228 4.7 40.3 1.0
C A:THR228 4.8 32.5 1.0
O A:HIS204 4.8 40.2 1.0
C A:HIS204 4.8 44.4 1.0
N A:HIS229 4.9 31.1 1.0
CA A:HIS229 4.9 38.4 1.0
N A:HIS204 4.9 47.1 1.0
CD2 A:LEU232 4.9 36.8 1.0
O A:MET202 4.9 40.8 1.0
N A:ARG233 4.9 41.7 1.0
C A:LEU232 4.9 37.5 1.0
CD A:LYS230 5.0 41.1 1.0

Sodium binding site 2 out of 3 in 6tgh

Go back to Sodium Binding Sites List in 6tgh
Sodium binding site 2 out of 3 in the Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:49.2
occ:1.00
 O C:ALA203 2.6 43.5 1.0
O C:HIS229 2.9 55.7 1.0
N C:LEU232 3.2 46.0 1.0
N C:THR231 3.4 47.2 1.0
CB C:LEU232 3.4 41.9 1.0
CB C:ALA206 3.5 39.5 1.0
CB C:LYS230 3.6 44.3 1.0
OG1 C:THR231 3.6 42.7 1.0
C C:HIS229 3.7 50.1 1.0
O C:THR227 3.7 43.2 1.0
C C:LYS230 3.8 44.4 1.0
C C:ALA203 3.8 40.3 1.0
CA C:LEU232 3.9 43.2 1.0
CA C:LYS230 4.0 45.2 1.0
OG1 C:THR227 4.0 41.2 1.0
N C:ALA206 4.1 36.4 1.0
C C:THR231 4.1 46.4 1.0
CA C:THR231 4.1 40.9 1.0
N C:GLY207 4.2 42.6 1.0
OG1 C:THR226 4.2 44.3 1.0
N C:LYS230 4.2 49.3 1.0
CA C:ALA206 4.2 36.1 1.0
CG C:LYS230 4.4 42.0 1.0
CB C:THR231 4.4 41.7 1.0
CA C:ALA203 4.5 41.6 1.0
O C:LYS230 4.5 51.2 1.0
O C:HIS204 4.5 41.7 1.0
C C:ALA206 4.6 35.2 1.0
C C:THR227 4.7 36.9 1.0
C C:HIS204 4.7 43.9 1.0
O C:MET202 4.7 44.8 1.0
CG C:LEU232 4.8 43.7 1.0
N C:HIS204 4.8 40.3 1.0
CD C:LYS230 4.8 47.0 1.0
CA C:HIS229 4.9 47.1 1.0
N C:HIS229 4.9 38.0 1.0
C C:LEU232 5.0 40.0 1.0
CD2 C:LEU232 5.0 42.8 1.0
N C:ARG233 5.0 43.2 1.0
C C:THR228 5.0 44.8 1.0
CA C:HIS204 5.0 45.8 1.0

Sodium binding site 3 out of 3 in 6tgh

Go back to Sodium Binding Sites List in 6tgh
Sodium binding site 3 out of 3 in the Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Shmt From Streptococcus Thermophilus TYR55THR Variant in Complex with D-Serine Both As External Aldimine and As Non-Covalent Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:48.8
occ:1.00
 O B:HIS229 2.7 46.8 1.0
O B:ALA203 2.8 41.6 1.0
N B:LEU232 3.2 35.5 1.0
N B:THR231 3.4 43.0 1.0
CB B:LEU232 3.4 38.4 1.0
CB B:LYS230 3.4 44.0 1.0
O B:THR227 3.6 41.1 1.0
C B:HIS229 3.6 43.3 1.0
CB B:ALA206 3.6 36.8 1.0
C B:LYS230 3.7 44.9 1.0
OG1 B:THR231 3.7 43.9 1.0
CA B:LYS230 3.9 42.7 1.0
CA B:LEU232 3.9 39.8 1.0
C B:ALA203 3.9 43.1 1.0
OG1 B:THR227 4.0 36.9 1.0
N B:LYS230 4.0 39.6 1.0
C B:THR231 4.1 40.2 1.0
CA B:THR231 4.2 41.6 1.0
N B:ALA206 4.2 34.2 1.0
OG1 B:THR226 4.2 37.5 1.0
CA B:ALA206 4.4 32.9 1.0
N B:GLY207 4.4 33.7 1.0
C B:THR227 4.5 41.4 1.0
O B:LYS230 4.5 48.8 1.0
CB B:THR231 4.6 41.0 1.0
CA B:ALA203 4.6 44.6 1.0
CG B:LYS230 4.6 46.2 1.0
CG B:LEU232 4.7 37.9 1.0
O B:THR228 4.7 43.0 1.0
C B:ALA206 4.8 35.4 1.0
C B:THR228 4.8 41.3 1.0
CA B:HIS229 4.8 41.4 1.0
O B:HIS204 4.8 41.6 1.0
CD B:LYS230 4.8 43.9 1.0
N B:HIS229 4.8 38.0 1.0
C B:HIS204 4.8 43.9 1.0
CD2 B:LEU232 4.9 40.1 1.0
C B:LEU232 4.9 44.4 1.0
N B:ARG233 4.9 46.6 1.0
N B:HIS204 5.0 39.5 1.0

Reference:

G.Petrillo, K.Hernandez, J.Bujons, P.Clapes, I.Uson. Structural Insights Into Nucleophile Substrate Specificity in Variants of N-Serine Hydroxymethyltransferase From Streptococcus Thermophilus To Be Published.
Page generated: Tue Oct 8 13:57:19 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