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Potassium in PDB 3du0: E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site

Enzymatic activity of E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site

All present enzymatic activity of E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site:
4.2.1.52;

Protein crystallography data

The structure of E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site, PDB code: 3du0 was solved by R.C.J.Dobson, S.R.A.Devenish, J.A.Gerrard, G.B.Jameson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.14 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.950, 120.950, 110.030, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 24.5

Other elements in 3du0:

The structure of E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site (pdb code 3du0). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site, PDB code: 3du0:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 3du0

Go back to Potassium Binding Sites List in 3du0
Potassium binding site 1 out of 4 in the E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, 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 E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K293

b:35.2
occ:1.00
 O A:ALA152 2.7 29.0 1.0
O A:ILE157 2.8 28.7 1.0
O A:VAL154 2.8 35.3 1.0
O A:LYS155 3.1 32.6 1.0
O A:HOH553 3.1 39.7 1.0
C A:LYS155 3.7 33.8 1.0
C A:ILE157 3.8 27.4 1.0
C A:ALA152 3.8 28.6 1.0
C A:VAL154 3.8 34.3 1.0
O A:HOH457 4.0 44.3 1.0
CA A:LYS155 4.1 36.0 1.0
N A:ILE157 4.2 29.9 1.0
N A:LYS155 4.4 34.6 1.0
CA A:ALA152 4.4 27.2 1.0
CA A:ILE157 4.5 28.0 1.0
CG2 A:ILE158 4.5 25.8 1.0
N A:ASN156 4.6 32.3 1.0
N A:ILE158 4.7 26.8 1.0
CA A:ILE158 4.7 26.4 1.0
N A:VAL154 4.7 34.0 1.0
C A:LYS153 4.7 32.8 1.0
N A:LYS153 4.7 28.4 1.0
CA A:VAL154 4.9 33.3 1.0
CA A:LYS153 5.0 31.9 1.0
CB A:ILE157 5.0 27.6 1.0
C A:ASN156 5.0 31.1 1.0

Potassium binding site 2 out of 4 in 3du0

Go back to Potassium Binding Sites List in 3du0
Potassium binding site 2 out of 4 in the E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, 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 E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K294

b:41.3
occ:1.00
 O A:LEU51 2.8 22.1 1.0
O A:HOH382 2.9 30.5 1.0
O A:SER48 3.0 26.4 1.0
O A:ALA49 3.0 24.4 1.0
O3 A:GOL296 3.0 30.1 1.0
O B:HOH413 3.1 28.2 1.0
O A:HOH381 3.1 37.2 1.0
C3 A:GOL296 3.4 31.6 1.0
O A:HOH329 3.4 31.5 1.0
C A:ALA49 3.4 23.6 1.0
C A:LEU51 3.8 22.4 1.0
CA A:ALA49 3.9 23.7 1.0
C A:SER48 4.0 23.4 1.0
N A:LEU51 4.1 19.9 1.0
N A:THR50 4.2 23.4 1.0
O3 A:GOL295 4.4 28.8 1.0
N A:ALA49 4.5 23.2 1.0
O B:HOH370 4.5 29.4 1.0
C A:THR50 4.6 21.3 1.0
CA A:LEU51 4.6 21.4 1.0
CA A:THR50 4.6 21.1 1.0
C2 A:GOL296 4.6 28.9 1.0
O2 A:GOL295 4.6 31.4 1.0
N A:ASN52 4.7 21.2 1.0
O2 A:GOL296 4.7 32.2 1.0
CA A:ASN52 4.8 24.5 1.0
OD1 B:ASN80 4.9 20.0 1.0

Potassium binding site 3 out of 4 in 3du0

Go back to Potassium Binding Sites List in 3du0
Potassium binding site 3 out of 4 in the E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, 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 E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K293

b:31.9
occ:1.00
 O B:ILE157 2.6 24.7 1.0
O B:ALA152 2.6 25.5 1.0
O B:VAL154 2.7 31.9 1.0
O B:HOH469 3.0 37.4 1.0
O B:HOH551 3.1 40.3 1.0
O B:LYS155 3.3 32.3 1.0
C B:ILE157 3.7 24.1 1.0
C B:ALA152 3.7 25.6 1.0
C B:VAL154 3.8 31.6 1.0
C B:LYS155 3.8 32.2 1.0
O B:HOH537 3.9 40.7 1.0
N B:ILE157 4.2 24.5 1.0
CA B:LYS155 4.2 33.3 1.0
CA B:ALA152 4.4 24.6 1.0
CA B:ILE157 4.4 24.4 1.0
N B:LYS155 4.5 32.5 1.0
CA B:ILE158 4.5 23.5 1.0
N B:ILE158 4.5 23.1 1.0
CG2 B:ILE158 4.5 24.6 1.0
N B:VAL154 4.6 30.6 1.0
N B:ASN156 4.7 30.4 1.0
O B:HOH549 4.7 42.5 1.0
C B:LYS153 4.7 29.4 1.0
N B:LYS153 4.8 27.7 1.0
CA B:VAL154 4.8 29.9 1.0
CD1 B:PHE181 4.9 20.7 1.0
CB B:ILE157 4.9 23.2 1.0
O B:LYS153 5.0 31.4 1.0
CB B:ALA152 5.0 23.5 1.0
C B:ASN156 5.0 26.4 1.0
CA B:LYS153 5.0 28.3 1.0

Potassium binding site 4 out of 4 in 3du0

Go back to Potassium Binding Sites List in 3du0
Potassium binding site 4 out of 4 in the E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, 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 E. Coli Dihydrodipicolinate Synthase with First Substrate, Pyruvate, Bound in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K294

b:47.1
occ:1.00
 O B:HOH412 2.6 35.7 1.0
O A:HOH383 2.7 34.3 1.0
O B:LEU51 2.8 28.6 1.0
O B:SER48 2.8 26.1 1.0
O B:ALA49 3.0 26.8 1.0
O A:HOH384 3.1 35.0 1.0
O B:HOH435 3.4 37.3 1.0
C B:ALA49 3.5 26.6 1.0
O1 A:GOL296 3.6 30.7 1.0
C B:LEU51 3.9 28.7 1.0
C B:SER48 4.0 26.1 1.0
CA B:ALA49 4.0 25.5 1.0
N B:LEU51 4.2 27.0 1.0
O1 B:GOL295 4.3 29.2 1.0
N B:THR50 4.3 26.8 1.0
O2 B:GOL295 4.4 30.6 1.0
N B:ALA49 4.4 25.8 1.0
C1 A:GOL296 4.5 27.4 1.0
CA B:LEU51 4.7 28.0 1.0
N B:ASN52 4.8 30.5 1.0
CA B:THR50 4.8 25.3 1.0
CA B:ASN52 4.8 33.5 1.0
C B:THR50 4.8 27.1 1.0
O B:HOH472 4.9 30.9 1.0

Reference:

S.R.Devenish, J.A.Gerrard, G.B.Jameson, R.C.Dobson. The High-Resolution Structure of Dihydrodipicolinate Synthase From Escherichia Coli Bound to Its First Substrate, Pyruvate. Acta Crystallogr.,Sect.F V. 64 1092 2008.
ISSN: ESSN 1744-3091
PubMed: 19052357
DOI: 10.1107/S1744309108033654
Page generated: Sat Aug 9 04:42:38 2025

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