Atomistry » Potassium » PDB 3gvx-3irp » 3i7r
Atomistry »
  Potassium »
    PDB 3gvx-3irp »
      3i7r »

Potassium in PDB 3i7r: Dihydrodipicolinate Synthase - K161R

Enzymatic activity of Dihydrodipicolinate Synthase - K161R

All present enzymatic activity of Dihydrodipicolinate Synthase - K161R:
4.2.1.52;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase - K161R, PDB code: 3i7r was solved by R.C.J.Dobson, G.B.Jameson, J.A.Gerrard, T.P.Soares Da Costa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.92 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.435, 121.435, 111.037, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 23

Other elements in 3i7r:

The structure of Dihydrodipicolinate Synthase - K161R also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Dihydrodipicolinate Synthase - K161R (pdb code 3i7r). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Dihydrodipicolinate Synthase - K161R, PDB code: 3i7r:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 3i7r

Go back to Potassium Binding Sites List in 3i7r
Potassium binding site 1 out of 4 in the Dihydrodipicolinate Synthase - K161R


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Dihydrodipicolinate Synthase - K161R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K293

b:34.7
occ:1.00
 O A:VAL154 2.8 27.9 1.0
O A:ALA152 2.8 24.7 1.0
O A:ILE157 2.8 22.8 1.0
O A:HOH428 2.9 46.8 1.0
O A:LYS155 3.3 27.8 1.0
C A:VAL154 3.8 27.6 1.0
C A:LYS155 3.8 27.6 1.0
C A:ILE157 3.8 23.5 1.0
C A:ALA152 3.8 24.6 1.0
CA A:LYS155 4.2 28.2 1.0
N A:ILE157 4.3 24.1 1.0
N A:LYS155 4.4 27.8 1.0
CA A:ALA152 4.5 24.2 1.0
N A:VAL154 4.6 27.2 1.0
CA A:ILE157 4.6 23.8 1.0
N A:ASN156 4.7 26.3 1.0
CA A:ILE158 4.7 23.5 1.0
C A:LYS153 4.7 27.0 1.0
N A:ILE158 4.7 23.6 1.0
CG2 A:ILE158 4.7 24.1 1.0
CA A:VAL154 4.8 27.3 1.0
N A:LYS153 4.8 25.6 1.0
CD1 A:PHE181 5.0 26.1 1.0
O A:LYS153 5.0 27.0 1.0

Potassium binding site 2 out of 4 in 3i7r

Go back to Potassium Binding Sites List in 3i7r
Potassium binding site 2 out of 4 in the Dihydrodipicolinate Synthase - K161R


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Dihydrodipicolinate Synthase - K161R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K294

b:40.6
occ:1.00
 O A:LEU51 2.7 21.2 1.0
O A:SER48 2.9 21.1 1.0
O3 A:GOL295 2.9 19.9 0.5
O A:HOH469 3.0 43.0 1.0
O A:HOH440 3.1 45.6 1.0
O3 A:GOL295 3.1 29.9 0.5
O A:ALA49 3.2 20.2 1.0
C A:ALA49 3.7 20.4 1.0
C3 A:GOL295 3.8 24.3 0.5
C A:LEU51 3.9 21.6 1.0
O2 A:GOL295 3.9 24.8 0.5
C A:SER48 4.0 20.5 1.0
CA A:ALA49 4.1 20.4 1.0
C3 A:GOL295 4.2 30.3 0.5
N A:LEU51 4.4 20.9 1.0
N A:THR50 4.4 20.4 1.0
C2 A:GOL295 4.5 24.4 0.5
O2 A:GOL298 4.5 43.0 1.0
N A:ALA49 4.6 20.3 1.0
O3 A:GOL298 4.6 34.5 1.0
CA A:ASN52 4.6 21.8 1.0
N A:ASN52 4.7 21.9 1.0
CA A:LEU51 4.8 21.5 1.0
O A:HOH429 4.9 30.0 1.0
C A:THR50 4.9 21.1 1.0
CA A:THR50 5.0 20.8 1.0
O A:HOH464 5.0 32.7 1.0

Potassium binding site 3 out of 4 in 3i7r

Go back to Potassium Binding Sites List in 3i7r
Potassium binding site 3 out of 4 in the Dihydrodipicolinate Synthase - K161R


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Dihydrodipicolinate Synthase - K161R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K293

b:28.9
occ:1.00
 O B:ILE157 2.7 20.8 1.0
O B:VAL154 2.7 26.4 1.0
O B:ALA152 2.7 22.0 1.0
O B:LYS155 3.1 25.4 1.0
C B:LYS155 3.7 26.0 1.0
C B:ILE157 3.7 21.0 1.0
C B:VAL154 3.7 26.4 1.0
C B:ALA152 3.8 22.5 1.0
CA B:LYS155 4.1 26.9 1.0
N B:ILE157 4.2 21.4 1.0
N B:LYS155 4.4 26.5 1.0
CA B:ALA152 4.4 22.0 1.0
CA B:ILE157 4.5 21.1 1.0
N B:VAL154 4.5 25.9 1.0
C B:LYS153 4.6 25.7 1.0
N B:ASN156 4.6 24.4 1.0
N B:ILE158 4.6 21.4 1.0
CA B:ILE158 4.7 21.4 1.0
N B:LYS153 4.8 23.8 1.0
CA B:VAL154 4.8 25.7 1.0
CD1 B:PHE181 4.9 21.0 1.0
O B:HOH342 4.9 36.3 1.0
CB B:ILE157 4.9 21.0 1.0
O B:LYS153 4.9 25.9 1.0
CA B:LYS153 5.0 25.4 1.0
C B:ASN156 5.0 22.2 1.0

Potassium binding site 4 out of 4 in 3i7r

Go back to Potassium Binding Sites List in 3i7r
Potassium binding site 4 out of 4 in the Dihydrodipicolinate Synthase - K161R


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Dihydrodipicolinate Synthase - K161R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K294

b:43.2
occ:1.00
 O B:THR126 2.7 25.0 1.0
O B:HOH438 2.8 27.4 1.0
O B:HOH343 2.8 35.3 1.0
O B:ALA123 2.9 19.2 1.0
O B:HOH378 3.0 37.2 1.0
O B:GLU124 3.4 22.4 1.0
C B:GLU124 3.8 22.0 1.0
C B:THR126 3.9 24.6 1.0
ND2 B:ASN156 3.9 26.8 1.0
OD1 B:ASN156 3.9 26.7 1.0
C B:ALA123 3.9 19.0 1.0
CA B:GLU124 4.0 21.1 1.0
CG B:ASN156 4.1 24.3 1.0
N B:THR126 4.3 23.7 1.0
N B:GLU124 4.4 19.9 1.0
OD1 B:ASP127 4.5 32.0 1.0
N B:HIS125 4.6 22.6 1.0
N B:ASP127 4.7 25.3 1.0
CA B:THR126 4.7 24.0 1.0
CA B:ASP127 4.8 26.0 1.0

Reference:

T.P.Soares Da Costa, A.C.Muscroft-Taylor, R.C.Dobson, S.R.Devenish, G.B.Jameson, J.A.Gerrard. How Essential Is the 'Essential' Active-Site Lysine in Dihydrodipicolinate Synthase? Biochimie V. 92 837 2010.
ISSN: ISSN 0300-9084
PubMed: 20353808
DOI: 10.1016/J.BIOCHI.2010.03.004
Page generated: Mon Aug 12 08:30:02 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy