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Potassium in PDB 3i7s: Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site.

Enzymatic activity of Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site.

All present enzymatic activity of Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site.:
4.2.1.52;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site., PDB code: 3i7s 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) 32.17 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.881, 120.881, 110.500, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 23.6

Potassium Binding Sites:

The binding sites of Potassium atom in the Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site. (pdb code 3i7s). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site., PDB code: 3i7s:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 3i7s

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Potassium binding site 1 out of 6 in the Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K295

b:39.5
occ:1.00
 O A:ILE157 2.7 28.3 1.0
O A:VAL154 2.8 33.0 1.0
O A:ALA152 2.8 29.3 1.0
O A:LYS155 3.2 32.9 1.0
C A:ILE157 3.8 28.3 1.0
C A:ALA152 3.9 29.7 1.0
C A:VAL154 3.9 32.9 1.0
C A:LYS155 3.9 32.7 1.0
CA A:LYS155 4.3 33.1 1.0
N A:ILE157 4.3 29.9 1.0
N A:LYS155 4.5 33.0 1.0
CA A:ALA152 4.5 29.4 1.0
CA A:ILE157 4.6 29.1 1.0
N A:VAL154 4.6 32.4 1.0
C A:LYS153 4.7 32.1 1.0
CA A:ILE158 4.7 27.9 1.0
N A:ASN156 4.7 32.1 1.0
N A:ILE158 4.8 28.3 1.0
CA A:LYS153 4.8 31.9 1.0
N A:LYS153 4.8 30.3 1.0
CG2 A:ILE158 4.8 28.5 1.0
CA A:VAL154 4.9 32.5 1.0
CD1 A:PHE181 5.0 29.3 1.0

Potassium binding site 2 out of 6 in 3i7s

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Potassium binding site 2 out of 6 in the Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K296

b:49.2
occ:1.00
 O A:HOH360 2.5 29.7 1.0
O A:LEU51 2.7 25.5 1.0
O A:HOH361 2.8 39.0 1.0
O3 A:GOL297 2.9 30.0 0.4
O A:SER48 2.9 24.9 1.0
O3 A:GOL297 3.0 16.6 0.6
O A:ALA49 3.0 24.8 1.0
C3 A:GOL297 3.4 28.1 0.4
C A:ALA49 3.5 25.2 1.0
C3 A:GOL297 3.5 20.0 0.6
C A:LEU51 3.8 26.0 1.0
CA A:ALA49 3.9 25.3 1.0
C A:SER48 4.0 25.0 1.0
N A:LEU51 4.2 25.6 1.0
N A:THR50 4.3 25.4 1.0
O3 A:GOL293 4.3 36.8 1.0
N A:ALA49 4.5 24.8 1.0
C2 A:GOL297 4.5 16.3 0.6
O2 A:GOL293 4.6 35.1 1.0
O2 A:GOL297 4.6 17.4 0.6
CA A:LEU51 4.6 26.0 1.0
N A:ASN52 4.7 26.2 1.0
CA A:ASN52 4.7 25.9 1.0
C A:THR50 4.8 25.5 1.0
CA A:THR50 4.8 25.8 1.0
C2 A:GOL297 4.9 26.8 0.4

Potassium binding site 3 out of 6 in 3i7s

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Potassium binding site 3 out of 6 in the Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K295

b:66.7
occ:1.00
 NE2 B:HIS125 3.3 28.5 1.0
O B:HOH395 4.1 33.3 1.0
CE1 B:HIS125 4.1 27.7 1.0
CD2 B:HIS125 4.3 27.5 1.0
CB B:GLU124 4.4 28.0 1.0
CG B:GLU124 4.5 35.2 1.0
CA B:ALA121 4.6 22.9 1.0
CB B:ALA121 4.7 22.6 1.0
O B:HOH392 4.9 42.6 1.0

Potassium binding site 4 out of 6 in 3i7s

Go back to Potassium Binding Sites List in 3i7s
Potassium binding site 4 out of 6 in the Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K296

b:55.5
occ:1.00
 O B:LEU51 2.8 29.9 1.0
O B:HOH398 3.0 44.5 1.0
O B:SER48 3.1 24.6 1.0
O A:HOH301 3.1 22.6 1.0
O B:ALA49 3.3 26.9 1.0
C B:ALA49 3.8 26.7 1.0
C B:LEU51 3.9 30.8 1.0
C B:SER48 4.2 25.0 1.0
CA B:ALA49 4.2 26.4 1.0
O1 A:GOL297 4.3 21.4 0.6
N B:LEU51 4.4 28.9 1.0
O2 B:GOL293 4.5 33.6 1.0
CA B:ASN52 4.6 33.8 1.0
N B:THR50 4.6 27.0 1.0
C1 A:GOL297 4.6 28.5 0.4
N B:ASN52 4.7 32.1 1.0
N B:ALA49 4.7 25.7 1.0
CD2 B:HIS53 4.7 39.1 1.0
C1 A:GOL297 4.8 20.3 0.6
O3 B:GOL293 4.8 31.4 1.0
CA B:LEU51 4.9 30.1 1.0

Potassium binding site 5 out of 6 in 3i7s

Go back to Potassium Binding Sites List in 3i7s
Potassium binding site 5 out of 6 in the Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K298

b:69.9
occ:1.00
 OE1 B:GLU84 3.2 23.9 0.5
ND1 B:HIS53 4.0 40.3 1.0
OG B:SER87 4.1 30.7 1.0
CD B:GLU84 4.1 25.8 0.5
OE2 B:GLU84 4.3 26.9 0.5
CE1 B:HIS53 4.7 40.2 1.0
CG B:HIS53 5.0 38.1 1.0

Potassium binding site 6 out of 6 in 3i7s

Go back to Potassium Binding Sites List in 3i7s
Potassium binding site 6 out of 6 in the Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Dihydrodipicolinate Synthase Mutant - K161A - with the Substrate Pyruvate Bound in the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K299

b:30.1
occ:1.00
 O B:ALA152 2.6 26.4 1.0
O B:VAL154 2.6 29.2 1.0
O B:ILE157 2.7 23.0 1.0
O B:LYS155 3.4 28.2 1.0
C B:VAL154 3.7 29.4 1.0
C B:ALA152 3.7 27.4 1.0
C B:ILE157 3.8 23.3 1.0
C B:LYS155 3.8 28.7 1.0
CA B:LYS155 4.1 30.2 1.0
N B:ILE157 4.3 23.6 1.0
N B:LYS155 4.3 29.9 1.0
CA B:ALA152 4.4 27.1 1.0
N B:VAL154 4.5 28.5 1.0
C B:LYS153 4.6 29.1 1.0
CA B:ILE157 4.6 23.0 1.0
N B:ASN156 4.6 26.8 1.0
CA B:ILE158 4.6 23.8 1.0
N B:ILE158 4.7 23.4 1.0
N B:LYS153 4.7 28.0 1.0
CA B:VAL154 4.7 28.9 1.0
CD1 B:PHE181 4.8 24.9 1.0
CA B:LYS153 4.9 29.2 1.0
O B:LYS153 4.9 29.0 1.0
CB B:ILE157 4.9 22.6 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: Sun Dec 13 23:19:38 2020

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