Atomistry » Sodium » PDB 8fry-8g2e » 8g1y
Atomistry »
  Sodium »
    PDB 8fry-8g2e »
      8g1y »

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: Wed Oct 9 12:00:44 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