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Sodium in PDB 8g1y: Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate.

Enzymatic activity of Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate.

All present enzymatic activity of Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate.:
4.2.3.1;

Protein crystallography data

The structure of Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate., PDB code: 8g1y was solved by G.Minasov, L.Shuvalova, O.Kiryukhina, K.J.F.Satchell, Center Forstructural Biology Of Infectious Diseases (Csbid), Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.29 / 1.43
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.464, 81.413, 139.465, 90, 94.6, 90
R / Rfree (%) 15.7 / 17.7

Other elements in 8g1y:

The structure of Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate. (pdb code 8g1y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate., PDB code: 8g1y:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8g1y

Go back to Sodium Binding Sites List in 8g1y
Sodium binding site 1 out of 5 in the Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:27.4
occ:1.00
 O A:HOH947 2.3 27.9 0.5
O A:HOH904 2.3 26.8 1.0
O A:HOH1008 2.3 31.1 1.0
O A:VAL40 2.3 20.8 1.0
O A:ILE281 2.4 14.7 1.0
O A:HOH1046 2.4 39.7 1.0
C A:ILE281 3.4 13.8 1.0
C A:VAL40 3.5 20.8 1.0
N A:VAL40 4.0 21.4 1.0
CA A:GLY282 4.0 13.1 1.0
O A:HOH1011 4.1 46.3 1.0
N A:GLY282 4.2 12.9 1.0
CA A:VAL40 4.2 21.3 1.0
O A:HOH874 4.3 41.2 1.0
CB A:VAL40 4.4 21.1 1.0
O A:HOH754 4.4 33.5 1.0
CA A:ILE281 4.4 14.2 1.0
N A:LEU42 4.5 18.7 1.0
N A:ASP41 4.5 20.6 1.0
CG A:LEU42 4.6 17.2 1.0
O A:HOH816 4.7 27.6 1.0
CA A:ASP41 4.7 22.3 1.0
CD1 A:LEU42 4.8 17.4 1.0
CB A:ILE281 4.9 14.7 1.0

Sodium binding site 2 out of 5 in 8g1y

Go back to Sodium Binding Sites List in 8g1y
Sodium binding site 2 out of 5 in the Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:25.7
occ:0.80
 OH A:TYR121 2.2 20.8 1.0
O A:HOH916 2.2 17.3 1.0
O A:HOH867 2.3 28.7 1.0
O A:HOH899 2.4 25.9 1.0
O B:HOH736 2.4 35.3 0.5
O A:HOH730 2.9 30.3 0.5
CZ A:TYR121 3.5 16.6 1.0
NZ B:LYS250 3.7 26.1 1.0
CE B:LYS250 3.9 23.4 1.0
CE2 A:TYR121 4.2 15.8 1.0
O A:ASN78 4.4 14.1 1.0
O A:HOH787 4.4 15.8 1.0
NZ A:LYS83 4.4 16.9 1.0
OD1 B:ASP49 4.4 19.0 1.0
O B:HOH1023 4.4 33.2 1.0
CE1 A:TYR121 4.5 15.3 1.0
CG2 A:VAL157 4.5 12.0 1.0
O A:HOH665 4.7 15.8 1.0
OD2 A:ASP81 4.8 18.4 1.0
OD1 A:ASN78 4.8 20.5 1.0
O A:HOH730 4.9 28.7 0.5
O A:ALA155 5.0 13.1 1.0

Sodium binding site 3 out of 5 in 8g1y

Go back to Sodium Binding Sites List in 8g1y
Sodium binding site 3 out of 5 in the Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:39.2
occ:1.00
 O A:HOH967 2.2 14.6 0.3
O A:HOH779 2.4 33.4 1.0
O A:HOH882 2.4 40.4 1.0
OE2 A:GLU258 2.6 14.2 0.3
OE1 A:GLU258 2.7 14.9 0.7
CD A:GLU258 3.3 13.9 0.3
OE1 A:GLU258 3.6 13.9 0.3
CD A:GLU258 3.7 14.3 0.7
NZ A:LYS418 3.8 23.1 1.0
OE2 A:GLU258 3.9 14.5 0.7
O A:HOH717 3.9 31.9 1.0
O A:HOH915 4.0 37.3 1.0
O A:HOH1074 4.5 23.4 1.0
CG A:GLU258 4.5 13.6 0.3
O A:HOH836 4.7 18.7 1.0
CE A:LYS418 4.8 20.5 1.0
CD A:LYS418 5.0 18.4 1.0

Sodium binding site 4 out of 5 in 8g1y

Go back to Sodium Binding Sites List in 8g1y
Sodium binding site 4 out of 5 in the Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:24.8
occ:1.00
 O B:VAL40 2.3 21.1 1.0
O B:HOH964 2.3 32.1 1.0
O B:HOH1035 2.3 27.3 0.5
O B:ILE281 2.3 14.9 1.0
O B:HOH988 2.4 29.6 1.0
C B:ILE281 3.4 13.8 1.0
C B:VAL40 3.4 21.4 1.0
N B:VAL40 3.9 21.8 1.0
CA B:GLY282 4.1 13.1 1.0
CA B:VAL40 4.1 21.5 1.0
N B:GLY282 4.2 13.0 1.0
O B:HOH980 4.3 39.9 1.0
O B:HOH774 4.3 25.1 0.5
CB B:VAL40 4.3 20.8 1.0
CA B:ILE281 4.4 13.8 1.0
O B:HOH833 4.4 31.4 1.0
N B:LEU42 4.5 18.4 1.0
N B:ASP41 4.5 21.2 1.0
CG B:LEU42 4.6 17.5 1.0
O B:HOH869 4.7 27.9 1.0
CA B:ASP41 4.7 23.1 1.0
CD1 B:LEU42 4.8 18.3 1.0
CB B:ILE281 4.8 13.8 1.0
CB B:LEU42 5.0 17.3 1.0

Sodium binding site 5 out of 5 in 8g1y

Go back to Sodium Binding Sites List in 8g1y
Sodium binding site 5 out of 5 in the Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:25.6
occ:0.80
 O B:THR478 2.3 18.3 1.0
O B:HOH1051 2.5 35.1 0.8
C B:THR478 3.3 18.4 1.0
CA B:VAL479 4.1 16.7 1.0
N B:VAL479 4.1 17.3 1.0
O B:HOH983 4.1 40.3 1.0
CB B:THR478 4.3 20.9 1.0
CA B:THR478 4.3 19.4 1.0
O B:HOH786 4.3 18.0 1.0
O B:HOH1051 4.5 20.7 0.2
N B:THR478 4.6 19.9 1.0
CG2 B:THR478 4.6 21.3 1.0
C B:VAL479 4.9 16.5 1.0

Reference:

G.Minasov, L.Shuvalova, O.Kiryukhina, K.J.F.Satchell, Center For Structural Biology Of Infectious Diseases (Csbid), Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the Threonine Synthase From Streptococcus Pneumoniae in Complex with Pyridoxal 5-Phosphate. To Be Published.
Page generated: Mon Aug 18 14:16:48 2025

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