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Potassium in PDB 7jza: Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site

Enzymatic activity of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site

All present enzymatic activity of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site, PDB code: 7jza was solved by A.J.Board, R.C.J.Dobson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.36 / 1.82
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.299, 121.299, 109.781, 90, 90, 120
R / Rfree (%) 13.6 / 16.5

Potassium Binding Sites:

The binding sites of Potassium atom in the Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site (pdb code 7jza). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site, PDB code: 7jza:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 7jza

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Potassium binding site 1 out of 3 in the Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:23.3
occ:1.00
 O A:HOH634 2.6 32.1 1.0
O A:ILE157 2.7 17.1 1.0
O A:ALA152 2.7 19.4 1.0
O A:VAL154 2.7 20.7 1.0
O A:HOH651 2.9 47.2 1.0
O A:LYS155 3.1 21.2 1.0
C A:LYS155 3.7 22.0 1.0
C A:ILE157 3.7 16.7 1.0
C A:VAL154 3.8 18.4 1.0
C A:ALA152 3.8 18.7 1.0
CA A:LYS155 4.0 25.7 1.0
N A:ILE157 4.1 14.8 1.0
O A:HOH624 4.2 46.8 1.0
N A:LYS155 4.4 22.3 1.0
CA A:ILE157 4.4 15.1 1.0
CA A:ALA152 4.4 17.1 1.0
N A:ASN156 4.6 18.5 1.0
N A:VAL154 4.6 20.6 1.0
C A:LYS153 4.6 25.2 1.0
N A:ILE158 4.6 15.2 1.0
CG2 A:ILE158 4.7 25.1 1.0
CA A:ILE158 4.7 16.3 1.0
N A:LYS153 4.8 16.8 1.0
CA A:VAL154 4.8 21.1 1.0
C A:ASN156 4.9 17.0 1.0
CB A:ILE157 4.9 15.3 1.0
O A:LYS153 4.9 23.7 1.0
CA A:LYS153 4.9 21.3 1.0

Potassium binding site 2 out of 3 in 7jza

Go back to Potassium Binding Sites List in 7jza
Potassium binding site 2 out of 3 in the Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:18.4
occ:1.00
 O B:ILE157 2.7 12.7 1.0
O B:ALA152 2.7 15.1 1.0
O B:HOH669 2.7 28.0 1.0
O B:VAL154 2.7 19.8 1.0
O B:HOH658 2.9 36.8 1.0
O B:HOH678 3.0 47.1 1.0
O B:LYS155 3.2 17.6 1.0
C B:LYS155 3.7 18.5 1.0
C B:ALA152 3.7 14.8 1.0
C B:ILE157 3.7 13.1 1.0
C B:VAL154 3.8 20.6 1.0
CA B:LYS155 4.0 20.9 1.0
N B:ILE157 4.2 12.9 1.0
O B:HOH593 4.3 38.7 1.0
N B:LYS155 4.3 19.6 1.0
CA B:ALA152 4.3 13.9 1.0
O B:HOH665 4.5 39.8 1.0
CA B:ILE157 4.5 12.8 1.0
N B:VAL154 4.6 18.4 1.0
N B:ASN156 4.6 15.3 1.0
C B:LYS153 4.6 23.2 1.0
N B:ILE158 4.7 12.6 1.0
CA B:ILE158 4.7 14.2 1.0
N B:LYS153 4.8 14.1 1.0
CA B:VAL154 4.8 18.9 1.0
CB B:ILE157 4.9 12.1 1.0
O B:LYS153 4.9 20.0 1.0
CA B:LYS153 4.9 17.8 1.0
CD1 B:PHE181 4.9 12.4 1.0
CB B:ALA152 5.0 14.3 1.0
CG2 B:ILE158 5.0 25.1 1.0

Potassium binding site 3 out of 3 in 7jza

Go back to Potassium Binding Sites List in 7jza
Potassium binding site 3 out of 3 in the Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Dihydrodipicolinate Synthase S48F Mutant with Lysine in the Allosteric Site, and Pyruvate and Succinic Semi-Aldehyde in the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K304

b:32.3
occ:1.00
 O B:THR126 2.7 20.7 1.0
O B:ALA123 2.8 15.4 1.0
O B:HOH409 2.8 39.2 1.0
O B:HOH662 2.9 44.6 1.0
O B:HOH541 2.9 23.8 1.0
O B:GLU124 3.3 22.5 1.0
C B:GLU124 3.7 21.9 1.0
ND2 B:ASN156 3.9 16.1 1.0
C B:THR126 3.9 19.2 1.0
C B:ALA123 3.9 15.0 1.0
OD1 B:ASN156 3.9 22.7 1.0
CA B:GLU124 3.9 18.1 1.0
O B:HOH571 4.0 39.8 1.0
CG B:ASN156 4.1 15.9 1.0
OD1 B:ASP127 4.3 38.0 1.0
N B:THR126 4.3 18.1 1.0
N B:GLU124 4.3 13.9 1.0
N B:HIS125 4.6 19.9 1.0
CA B:ASP127 4.6 19.5 1.0
N B:ASP127 4.6 18.6 1.0
CA B:THR126 4.7 18.4 1.0

Reference:

A.J.Board, R.C.J.Dobson. Mapping the Uncharted Water Channel of Dhdps To Be Published.
Page generated: Sat Aug 9 13:28:37 2025

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