Atomistry » Sodium » PDB 5syu-5tde » 5t26
Atomistry »
  Sodium »
    PDB 5syu-5tde »
      5t26 »

Sodium in PDB 5t26: Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.

Enzymatic activity of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.

All present enzymatic activity of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.:
4.3.3.7;

Protein crystallography data

The structure of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli., PDB code: 5t26 was solved by L.Chooback, L.M.Thomas, W.E.Karsten, C.D.Fleming, P.Seabourn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.51 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 56.714, 161.492, 137.325, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. (pdb code 5t26). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli., PDB code: 5t26:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5t26

Go back to Sodium Binding Sites List in 5t26
Sodium binding site 1 out of 7 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:19.8
occ:1.00
 O A:LEU243 2.5 11.0 1.0
OD1 A:ASN248 2.8 10.7 1.0
N A:VAL252 3.1 10.9 1.0
CD A:PRO251 3.3 12.1 1.0
CB A:VAL252 3.4 10.2 1.0
CG1 A:VAL252 3.4 9.5 1.0
C A:LEU243 3.6 11.7 1.0
CA A:PRO249 3.7 12.4 1.0
CB A:PRO251 3.7 11.3 1.0
CA A:ASN248 3.7 12.4 1.0
CG A:ASN248 3.7 11.5 1.0
N A:PRO251 3.8 12.0 1.0
CA A:VAL252 3.8 10.7 1.0
C A:PRO249 3.9 12.4 1.0
CG A:PRO251 3.9 11.2 1.0
CB A:ASN248 3.9 12.2 1.0
CB A:LEU243 3.9 12.8 1.0
C A:PRO251 4.0 11.6 1.0
CA A:PRO251 4.0 11.5 1.0
CA A:LEU243 4.0 12.4 1.0
CG1 A:VAL205 4.1 14.9 1.0
O A:PRO249 4.2 13.3 1.0
N A:ILE250 4.2 12.4 1.0
CD2 A:LEU243 4.6 12.4 1.0
C A:ILE250 4.6 12.5 1.0
N A:ASN248 4.6 11.9 1.0
N A:PRO249 4.6 12.4 1.0
C A:ASN248 4.7 12.8 1.0
CB A:PRO249 4.7 12.7 1.0
CG A:LEU243 4.8 12.7 1.0
N A:PHE244 4.8 12.1 1.0
CG2 A:VAL252 4.8 10.0 1.0
ND2 A:ASN248 5.0 10.8 1.0

Sodium binding site 2 out of 7 in 5t26

Go back to Sodium Binding Sites List in 5t26
Sodium binding site 2 out of 7 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:18.3
occ:1.00
 O A:THR45 2.7 10.8 1.0
OE1 A:GLU47 2.8 14.3 1.0
N A:THR11 2.9 11.4 1.0
CE A:LYS253 3.4 13.3 1.0
CA A:VAL10 3.5 11.3 1.0
CA A:GLY46 3.5 12.8 1.0
C A:GLY46 3.5 13.6 1.0
NZ A:LYS253 3.6 13.8 1.0
CD A:GLU47 3.7 13.2 1.0
C A:VAL10 3.7 11.6 1.0
CG A:GLU47 3.7 13.2 1.0
C A:THR45 3.7 11.6 1.0
CB A:VAL10 3.7 11.5 1.0
O A:THR11 3.8 12.1 1.0
CG A:PRO249 3.8 11.9 1.0
N A:GLU47 3.8 13.0 1.0
CA A:THR11 3.8 11.6 1.0
CB A:THR11 3.9 11.1 1.0
CB A:GLU47 4.0 13.0 1.0
O A:GLY46 4.0 14.2 1.0
N A:GLY46 4.0 11.9 1.0
C A:THR11 4.1 12.3 1.0
CD A:LYS253 4.2 13.0 1.0
CG1 A:VAL10 4.2 11.1 1.0
OG1 A:THR11 4.3 10.3 1.0
CB A:PRO249 4.3 12.7 1.0
CA A:GLU47 4.5 13.1 1.0
CG A:LYS253 4.7 13.0 1.0
N A:VAL10 4.8 10.7 1.0
OE2 A:GLU47 4.9 13.0 1.0
O A:VAL10 4.9 12.0 1.0

Sodium binding site 3 out of 7 in 5t26

Go back to Sodium Binding Sites List in 5t26
Sodium binding site 3 out of 7 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:20.0
occ:1.00
 OG A:SER5 2.7 14.4 1.0
OG1 A:THR36 2.8 14.6 1.0
O A:ALA211 2.8 14.8 1.0
CB A:SER5 3.3 14.1 1.0
CA A:THR36 3.6 15.0 1.0
CA A:ALA211 3.6 14.3 1.0
C A:ALA211 3.6 14.2 1.0
CB A:THR36 3.6 14.6 1.0
N A:ALA215 3.7 12.6 1.0
CB A:ALA211 3.8 14.3 1.0
CB A:ALA207 3.9 11.7 1.0
CB A:ALA215 3.9 12.7 1.0
CG2 A:THR36 3.9 14.0 1.0
CB A:MET214 3.9 12.4 1.0
N A:THR36 4.0 15.6 1.0
CA A:ALA215 4.1 12.9 1.0
O A:SER5 4.2 14.0 1.0
C A:MET214 4.3 13.5 1.0
CA A:SER5 4.5 14.0 1.0
C A:SER5 4.5 13.7 1.0
CA A:MET214 4.6 12.9 1.0
CA A:ALA207 4.8 11.3 1.0
O A:ALA207 4.8 10.9 1.0
C A:GLY35 4.8 14.8 1.0
N A:ARG212 4.8 14.8 1.0
C A:THR36 4.9 15.3 1.0
ND1 A:HIS31 4.9 12.6 1.0
N A:ALA211 4.9 13.6 1.0
O A:HOH460 4.9 12.7 1.0

Sodium binding site 4 out of 7 in 5t26

Go back to Sodium Binding Sites List in 5t26
Sodium binding site 4 out of 7 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:20.2
occ:1.00
 O A:THR139 2.7 11.5 1.0
O A:PRO105 2.7 13.5 1.0
N A:ARG109 2.9 14.9 1.0
CA A:ARG109 3.1 16.0 1.0
CB A:CYS141 3.1 19.6 1.0
N A:TYR107 3.3 15.0 1.0
C A:TYR106 3.5 14.0 1.0
CA A:TYR106 3.6 13.6 1.0
C A:PRO105 3.6 13.1 1.0
C A:THR139 3.7 11.9 1.0
CD A:PRO110 3.8 14.5 1.0
CG A:ARG109 3.9 20.0 1.0
N A:ASN108 3.9 14.6 1.0
N A:TYR106 3.9 12.9 1.0
C A:GLY140 4.0 13.5 1.0
CB A:ARG109 4.0 17.8 1.0
C A:TYR107 4.1 15.2 1.0
N A:CYS141 4.1 14.5 1.0
C A:ASN108 4.1 14.7 1.0
CA A:CYS141 4.2 16.1 1.0
SG A:CYS141 4.2 23.4 1.0
CA A:TYR107 4.2 16.0 1.0
O A:TYR106 4.3 13.2 1.0
C A:ARG109 4.3 15.3 1.0
CA A:GLY140 4.4 12.0 1.0
CD A:ARG109 4.4 24.1 1.0
O A:GLY140 4.4 12.5 1.0
N A:GLY140 4.4 11.4 1.0
OD1 A:ASN108 4.4 13.4 1.0
CB A:THR139 4.5 11.6 1.0
N A:PRO110 4.5 14.7 1.0
CA A:THR139 4.6 11.4 1.0
O A:TYR107 4.7 13.7 1.0
CA A:ASN108 4.7 15.0 1.0
OG1 A:THR139 4.9 10.7 1.0
CB A:TYR106 4.9 13.9 1.0
CA A:PRO105 4.9 12.6 1.0
CG A:PRO110 5.0 14.6 1.0

Sodium binding site 5 out of 7 in 5t26

Go back to Sodium Binding Sites List in 5t26
Sodium binding site 5 out of 7 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:16.2
occ:1.00
 OG A:SER185 2.6 11.2 1.0
O A:HOH471 2.7 7.7 1.0
OG A:SER190 2.7 9.7 1.0
CB A:SER185 3.4 11.9 1.0
CD2 A:PHE194 3.4 10.9 1.0
O A:SER190 3.6 12.5 1.0
CB A:PHE194 3.6 10.6 1.0
O A:ASP187 3.7 11.5 1.0
C A:SER190 3.7 11.2 1.0
CB A:ASP187 3.7 12.7 1.0
CB A:SER190 3.8 10.5 1.0
CG A:PHE194 3.8 10.6 1.0
N A:ALA191 4.0 10.4 1.0
CA A:SER185 4.1 12.0 1.0
CD2 A:LEU167 4.2 12.2 1.0
CA A:ALA191 4.2 10.8 1.0
N A:ASP187 4.3 12.3 1.0
CA A:SER190 4.3 10.7 1.0
O A:GLU162 4.3 12.0 1.0
CE2 A:PHE194 4.4 10.5 1.0
CA A:ASP187 4.4 12.5 1.0
OD2 A:ASP187 4.4 15.2 1.0
C A:ASP187 4.5 12.2 1.0
CG A:ASP187 4.6 13.8 1.0
CA A:GLY165 4.6 13.2 1.0
O A:HOH542 4.7 10.7 1.0
N A:GLY186 4.7 12.3 1.0
N A:SER190 4.8 10.6 1.0
CA A:PHE194 4.9 11.0 1.0
C A:SER185 4.9 12.0 1.0
CD1 A:PHE194 4.9 10.7 1.0
N A:GLY165 5.0 13.4 1.0

Sodium binding site 6 out of 7 in 5t26

Go back to Sodium Binding Sites List in 5t26
Sodium binding site 6 out of 7 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:19.2
occ:1.00
 OE1 B:GLU47 2.7 13.7 1.0
O B:THR45 2.7 11.8 1.0
N B:THR11 3.0 12.2 1.0
CE B:LYS253 3.5 13.3 1.0
C B:GLY46 3.5 12.6 1.0
CA B:GLY46 3.5 12.4 1.0
CA B:VAL10 3.6 12.1 1.0
CD B:GLU47 3.6 13.7 1.0
NZ B:LYS253 3.7 12.9 1.0
C B:THR45 3.7 12.3 1.0
O B:THR11 3.7 11.3 1.0
CG B:GLU47 3.7 12.8 1.0
CG B:PRO249 3.8 12.1 1.0
C B:VAL10 3.8 12.2 1.0
N B:GLU47 3.8 12.2 1.0
CA B:THR11 3.8 12.0 1.0
CB B:VAL10 3.8 12.2 1.0
CB B:THR11 3.9 11.7 1.0
O B:GLY46 3.9 12.3 1.0
CB B:GLU47 3.9 12.5 1.0
N B:GLY46 4.0 12.9 1.0
C B:THR11 4.0 12.1 1.0
CD B:LYS253 4.2 13.3 1.0
OG1 B:THR11 4.2 11.2 1.0
CG1 B:VAL10 4.3 12.2 1.0
CB B:PRO249 4.4 12.6 1.0
CA B:GLU47 4.5 12.5 1.0
CG B:LYS253 4.7 13.0 1.0
OE2 B:GLU47 4.8 12.9 1.0
N B:VAL10 4.9 11.6 1.0

Sodium binding site 7 out of 7 in 5t26

Go back to Sodium Binding Sites List in 5t26
Sodium binding site 7 out of 7 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:19.6
occ:1.00
 O B:LEU243 2.6 12.4 1.0
OD1 B:ASN248 2.9 13.9 1.0
N B:VAL252 3.0 11.2 1.0
CD B:PRO251 3.3 11.5 1.0
CB B:VAL252 3.3 10.9 1.0
CG1 B:VAL252 3.4 10.5 1.0
CB B:PRO251 3.6 10.9 1.0
C B:LEU243 3.6 12.6 1.0
N B:PRO251 3.7 11.6 1.0
CA B:VAL252 3.7 11.4 1.0
CA B:PRO249 3.7 12.4 1.0
CG B:PRO251 3.7 11.2 1.0
CG B:ASN248 3.8 15.1 1.0
CA B:ASN248 3.8 14.6 1.0
C B:PRO249 3.8 12.9 1.0
C B:PRO251 3.9 11.9 1.0
CA B:PRO251 3.9 11.4 1.0
CB B:LEU243 3.9 13.2 1.0
CB B:ASN248 4.0 15.3 1.0
CA B:LEU243 4.0 13.5 1.0
O B:PRO249 4.1 13.6 1.0
CG2 B:VAL205 4.1 17.5 1.0
N B:ILE250 4.2 12.0 1.0
CD2 B:LEU243 4.5 13.2 1.0
C B:ILE250 4.6 12.2 1.0
CG2 B:VAL252 4.7 10.6 1.0
N B:PRO249 4.7 13.0 1.0
CB B:PRO249 4.7 12.6 1.0
N B:ASN248 4.7 13.8 1.0
CG B:LEU243 4.7 12.6 1.0
C B:ASN248 4.7 14.2 1.0
N B:PHE244 4.8 13.0 1.0
C B:VAL252 4.9 11.7 1.0
O B:PRO251 5.0 12.0 1.0
ND2 B:ASN248 5.0 14.2 1.0

Reference:

L.Chooback, L.M.Thomas, W.E.Karsten, C.D.Fleming, P.Seabourn. Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. To Be Published.
Page generated: Tue Oct 8 00:00:54 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy