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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

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