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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

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