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Potassium in PDB 4eou: Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site

Enzymatic activity of Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site

All present enzymatic activity of Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site:
4.2.1.52;

Protein crystallography data

The structure of Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site, PDB code: 4eou was solved by B.A.Boughton, R.C.J.Dobson, C.A.Hutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.10 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.172, 121.172, 109.732, 90.00, 90.00, 120.00
R / Rfree (%) 14.3 / 19.8

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site (pdb code 4eou). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site, PDB code: 4eou:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4eou

Go back to Potassium Binding Sites List in 4eou
Potassium binding site 1 out of 4 in the Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:16.7
occ:1.00
 O A:ILE157 2.6 9.7 1.0
O A:VAL154 2.6 16.9 1.0
O A:ALA152 2.7 12.4 1.0
O A:HOH568 2.7 29.3 1.0
O A:HOH514 2.8 25.1 1.0
O A:HOH588 3.2 41.4 1.0
O A:LYS155 3.2 15.2 1.0
C A:ALA152 3.7 13.2 1.0
C A:ILE157 3.7 10.1 1.0
C A:VAL154 3.7 16.6 1.0
C A:LYS155 3.8 16.4 1.0
CA A:LYS155 4.1 18.2 1.0
N A:ILE157 4.1 10.6 1.0
CA A:ALA152 4.3 12.2 1.0
N A:LYS155 4.4 18.8 1.0
CA A:ILE157 4.5 10.1 1.0
N A:VAL154 4.5 16.3 1.0
C A:LYS153 4.6 16.6 1.0
N A:ASN156 4.6 15.1 1.0
O A:HOH601 4.6 34.9 1.0
N A:ILE158 4.7 10.0 1.0
CA A:ILE158 4.7 10.2 1.0
N A:LYS153 4.7 13.7 1.0
O A:HOH586 4.7 43.2 1.0
CA A:VAL154 4.8 15.5 1.0
CD1 A:PHE181 4.9 10.2 1.0
CB A:ILE157 4.9 9.6 1.0
CA A:LYS153 4.9 15.7 1.0
O A:LYS153 4.9 17.7 1.0

Potassium binding site 2 out of 4 in 4eou

Go back to Potassium Binding Sites List in 4eou
Potassium binding site 2 out of 4 in the Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K303

b:28.4
occ:1.00
 O A:THR126 2.7 17.5 1.0
O A:HOH512 2.8 15.9 1.0
O A:ALA123 2.9 11.8 1.0
O A:HOH557 3.2 36.8 1.0
O A:GLU124 3.2 19.4 1.0
OD1 A:ASN156 3.7 17.4 1.0
C A:GLU124 3.8 18.0 1.0
ND2 A:ASN156 3.8 17.0 1.0
C A:THR126 3.9 16.8 1.0
C A:ALA123 4.0 12.9 1.0
CG A:ASN156 4.0 16.4 1.0
CA A:GLU124 4.0 18.6 1.0
O A:HOH471 4.1 27.0 1.0
N A:THR126 4.3 15.0 1.0
OD1 A:ASP127 4.4 27.1 1.0
N A:GLU124 4.4 15.2 1.0
N A:HIS125 4.7 15.8 1.0
N A:ASP127 4.7 19.2 1.0
CA A:THR126 4.7 14.6 1.0
CA A:ASP127 4.8 20.4 1.0
OE1 A:GLU124 5.0 49.0 1.0

Potassium binding site 3 out of 4 in 4eou

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Potassium binding site 3 out of 4 in the Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:25.4
occ:1.00
 O B:ILE157 2.6 20.0 1.0
O B:VAL154 2.7 20.9 1.0
O B:ALA152 2.7 17.9 1.0
O B:HOH561 3.0 30.6 1.0
O B:LYS155 3.3 19.9 1.0
O B:HOH603 3.4 36.9 1.0
C B:ILE157 3.7 17.2 1.0
C B:ALA152 3.8 18.5 1.0
C B:VAL154 3.8 22.3 1.0
C B:LYS155 3.9 22.6 1.0
N B:ILE157 4.2 18.2 1.0
CA B:LYS155 4.3 25.1 1.0
CA B:ALA152 4.4 16.7 1.0
CA B:ILE157 4.4 16.8 1.0
N B:LYS155 4.4 23.7 1.0
N B:ILE158 4.6 16.6 1.0
C B:LYS153 4.6 23.6 1.0
CA B:ILE158 4.6 16.2 1.0
N B:VAL154 4.6 22.5 1.0
O B:HOH548 4.7 38.4 1.0
N B:LYS153 4.7 18.9 1.0
N B:ASN156 4.8 21.1 1.0
CD1 B:PHE181 4.8 17.6 1.0
CA B:VAL154 4.9 21.4 1.0
CA B:LYS153 4.9 21.5 1.0
CB B:ILE157 4.9 15.6 1.0
O B:LYS153 5.0 23.0 1.0
CB B:ALA152 5.0 15.2 1.0

Potassium binding site 4 out of 4 in 4eou

Go back to Potassium Binding Sites List in 4eou
Potassium binding site 4 out of 4 in the Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of E. Coli Dihydrodipicolinate Synthase with Pyruvate and Succinic Semi-Aldehyde Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K303

b:34.7
occ:1.00
 O B:THR126 2.6 20.2 1.0
O B:ALA123 2.8 17.3 1.0
O B:HOH500 2.9 26.1 1.0
C B:THR126 3.8 20.5 1.0
O B:GLU124 3.8 22.9 1.0
C B:ALA123 3.8 19.4 1.0
OD1 B:ASN156 3.8 24.4 1.0
CA B:GLU124 3.9 20.9 1.0
C B:GLU124 3.9 22.2 1.0
ND2 B:ASN156 4.0 21.6 1.0
CG B:ASN156 4.1 22.0 1.0
N B:THR126 4.1 20.6 1.0
N B:GLU124 4.3 19.4 1.0
OD1 B:ASP127 4.5 32.5 1.0
CA B:THR126 4.6 20.2 1.0
N B:HIS125 4.7 21.8 1.0
N B:ASP127 4.7 22.6 1.0
CA B:ASP127 4.8 24.5 1.0

Reference:

B.A.Boughton, R.C.Dobson, C.A.Hutton. The Crystal Structure of Dihydrodipicolinate Synthase From Escherichia Coli with Bound Pyruvate and Succinic Acid Semialdehyde: Unambiguous Resolution of the Stereochemistry of the Condensation Product. Proteins V. 80 2117 2012.
ISSN: ISSN 0887-3585
PubMed: 22552955
DOI: 10.1002/PROT.24106
Page generated: Mon Aug 12 10:40:19 2024

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