Potassium in PDB 7jz9: Dihydrodipicolinate Synthase S48F with Pyruvate and Succinic Semi- Aldehyde

Enzymatic activity of Dihydrodipicolinate Synthase S48F with Pyruvate and Succinic Semi- Aldehyde

All present enzymatic activity of Dihydrodipicolinate Synthase S48F with Pyruvate and Succinic Semi- Aldehyde:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase S48F with Pyruvate and Succinic Semi- Aldehyde, PDB code: 7jz9 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) 33.27 / 1.82
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.919, 120.919, 110.081, 90, 90, 120
R / Rfree (%) 14.3 / 17.1

Potassium Binding Sites:

The binding sites of Potassium atom in the Dihydrodipicolinate Synthase S48F with Pyruvate and Succinic Semi- Aldehyde (pdb code 7jz9). 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 with Pyruvate and Succinic Semi- Aldehyde, PDB code: 7jz9:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 7jz9

Go back to Potassium Binding Sites List in 7jz9
Potassium binding site 1 out of 3 in the Dihydrodipicolinate Synthase S48F with Pyruvate and Succinic Semi- Aldehyde


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 with Pyruvate and Succinic Semi- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:25.9
occ:1.00
 O A:ILE157 2.6 18.8 1.0
O A:VAL154 2.6 25.5 1.0
O A:HOH617 2.7 31.9 1.0
O A:ALA152 2.7 23.5 1.0
O A:HOH646 2.8 46.7 1.0
O A:LYS155 3.1 24.5 1.0
C A:LYS155 3.7 26.1 1.0
C A:ILE157 3.7 19.4 1.0
C A:VAL154 3.7 24.2 1.0
C A:ALA152 3.8 21.0 1.0
CA A:LYS155 4.0 27.6 1.0
N A:ILE157 4.1 18.9 1.0
O A:HOH609 4.2 46.1 1.0
N A:LYS155 4.3 27.0 1.0
CA A:ALA152 4.4 19.0 1.0
CA A:ILE157 4.4 18.2 1.0
N A:VAL154 4.5 25.2 1.0
N A:ASN156 4.5 21.1 1.0
N A:ILE158 4.6 17.6 1.0
C A:LYS153 4.6 28.3 1.0
CA A:ILE158 4.6 19.3 1.0
CG2 A:ILE158 4.7 27.7 1.0
N A:LYS153 4.8 19.1 1.0
CA A:VAL154 4.8 25.3 1.0
CB A:ILE157 4.9 18.2 1.0
C A:ASN156 4.9 21.2 1.0
O A:LYS153 4.9 25.5 1.0
CA A:LYS153 5.0 25.0 1.0

Potassium binding site 2 out of 3 in 7jz9

Go back to Potassium Binding Sites List in 7jz9
Potassium binding site 2 out of 3 in the Dihydrodipicolinate Synthase S48F with Pyruvate and Succinic Semi- Aldehyde


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 with Pyruvate and Succinic Semi- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K302

b:29.1
occ:1.00
 OD1 A:ASN80 2.6 16.1 1.0
O B:ALA49 2.6 25.5 1.0
OE2 A:GLU84 2.7 33.7 1.0
O3 B:GOL302 2.8 45.2 1.0
O B:HOH479 2.9 28.3 1.0
O A:HOH608 3.0 44.9 1.0
O B:HOH533 3.3 35.8 1.0
O A:HOH403 3.7 42.0 1.0
CD A:GLU84 3.7 43.8 1.0
CG A:ASN80 3.7 16.7 1.0
C B:ALA49 3.8 22.2 1.0
C3 B:GOL302 3.8 42.9 1.0
OE1 A:GLU84 3.9 58.0 1.0
ND2 A:ASN80 4.2 15.5 1.0
CA B:ALA49 4.4 20.7 1.0
CB A:ALA81 4.5 18.1 1.0
N A:ALA81 4.5 15.9 1.0
O2 B:GOL302 4.6 42.9 1.0
N B:THR50 4.8 17.8 1.0
N A:ASN80 4.9 15.2 1.0
C A:ASN80 4.9 17.2 1.0
CA B:THR50 5.0 18.4 1.0
O B:PHE48 5.0 21.7 1.0

Potassium binding site 3 out of 3 in 7jz9

Go back to Potassium Binding Sites List in 7jz9
Potassium binding site 3 out of 3 in the Dihydrodipicolinate Synthase S48F with Pyruvate and Succinic Semi- Aldehyde


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 with Pyruvate and Succinic Semi- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:20.6
occ:1.00
 O B:ILE157 2.6 15.8 1.0
O B:ALA152 2.6 17.0 1.0
O B:HOH665 2.7 30.1 1.0
O B:VAL154 2.7 22.5 1.0
O B:HOH645 2.9 51.4 1.0
O B:LYS155 3.2 19.0 1.0
C B:ALA152 3.7 16.0 1.0
C B:LYS155 3.7 20.8 1.0
C B:ILE157 3.7 15.6 1.0
C B:VAL154 3.8 22.0 1.0
CA B:LYS155 4.0 22.3 1.0
N B:ILE157 4.2 15.2 1.0
O B:HOH652 4.2 45.4 1.0
O B:HOH529 4.2 38.6 1.0
CA B:ALA152 4.3 17.4 1.0
N B:LYS155 4.4 21.8 1.0
CA B:ILE157 4.5 15.6 1.0
O B:HOH441 4.6 49.9 1.0
N B:ASN156 4.6 18.5 1.0
N B:VAL154 4.6 20.5 1.0
C B:LYS153 4.6 24.5 1.0
N B:ILE158 4.7 14.1 1.0
CA B:ILE158 4.7 16.7 1.0
N B:LYS153 4.7 15.8 1.0
CA B:VAL154 4.8 19.9 1.0
CB B:ILE157 4.9 15.1 1.0
CG2 B:ILE158 4.9 24.9 1.0
CD1 B:PHE181 4.9 14.5 1.0
CA B:LYS153 4.9 18.7 1.0
O B:LYS153 4.9 20.5 1.0
C B:ASN156 5.0 15.3 1.0
CB B:ALA152 5.0 16.5 1.0

Reference:

A.J.Board, R.C.J.Dobson. Mapping the Uncharted Water Channel of Dhdps To Be Published.
Page generated: Fri Sep 24 14:41:36 2021

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