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Sodium in PDB 5t25: Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.

Enzymatic activity of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.

All present enzymatic activity of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.:
4.3.3.7;

Protein crystallography data

The structure of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli., PDB code: 5t25 was solved by L.Chooback, L.M.Thomas, W.E.Karsten, C.D.Fleming, P.Seabourn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.81 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.647, 56.385, 101.530, 90.00, 127.62, 90.00
R / Rfree (%) 15.8 / 21.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. (pdb code 5t25). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli., PDB code: 5t25:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 5t25

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Sodium binding site 1 out of 10 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:18.9
occ:1.00
 OG A:SER185 2.5 13.2 1.0
OG A:SER190 2.7 14.7 1.0
O A:HOH518 2.8 12.1 1.0
CB A:SER185 3.3 12.9 1.0
CD2 A:PHE194 3.3 13.0 1.0
CB A:PHE194 3.4 11.1 1.0
O A:SER190 3.6 12.8 1.0
O A:ASP187 3.6 14.2 1.0
C A:SER190 3.7 11.8 1.0
CG A:PHE194 3.7 11.4 1.0
CB A:SER190 3.8 10.9 1.0
CB A:ASP187 3.9 14.5 1.0
N A:ALA191 4.0 12.7 1.0
CA A:ALA191 4.0 14.3 1.0
CA A:SER185 4.1 12.1 1.0
N A:ASP187 4.2 14.2 1.0
CA A:SER190 4.3 11.5 1.0
CD2 A:LEU167 4.3 10.6 1.0
CE2 A:PHE194 4.3 10.6 1.0
O A:GLU162 4.4 11.1 1.0
CA A:ASP187 4.4 13.7 1.0
C A:ASP187 4.5 13.0 1.0
OD2 A:ASP187 4.5 14.9 1.0
CA A:GLY165 4.7 15.6 1.0
N A:GLY186 4.7 13.9 1.0
CG A:ASP187 4.7 19.3 1.0
CA A:PHE194 4.7 12.3 1.0
CD1 A:PHE194 4.8 11.9 1.0
N A:SER190 4.8 13.4 1.0
O A:HOH560 4.8 12.4 1.0
C A:SER185 4.8 9.6 1.0
N A:PHE194 4.9 14.2 1.0
CB A:ALA191 5.0 12.1 1.0
N A:GLY165 5.0 17.7 1.0

Sodium binding site 2 out of 10 in 5t25

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Sodium binding site 2 out of 10 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:23.3
occ:1.00
 OG1 A:THR77 2.6 16.5 1.0
O A:HOH452 2.7 16.7 1.0
OG1 A:THR89 2.7 17.8 1.0
OE1 A:GLN130 2.7 17.6 1.0
CB A:THR77 3.4 16.1 1.0
CG2 A:ILE122 3.4 14.2 1.0
CB A:CYS100 3.5 17.8 1.0
CD A:GLN130 3.6 17.6 1.0
CB A:THR89 3.8 19.0 1.0
NE2 A:GLN130 3.9 17.0 1.0
CB A:THR102 3.9 14.1 1.0
CG2 A:THR89 3.9 19.3 1.0
SG A:CYS100 3.9 18.4 1.0
CG2 A:THR77 4.2 12.3 1.0
OG1 A:THR102 4.2 16.4 1.0
CG2 A:THR102 4.3 11.7 1.0
O A:THR77 4.4 14.6 1.0
CA A:THR77 4.6 14.8 1.0
CA A:THR89 4.7 17.8 1.0
C A:THR77 4.7 17.6 1.0
O A:ALA85 4.8 17.7 1.0
CB A:ILE122 4.8 16.1 1.0
CA A:CYS100 4.9 11.3 1.0

Sodium binding site 3 out of 10 in 5t25

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Sodium binding site 3 out of 10 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:22.9
occ:1.00
 O A:HOH611 2.3 35.4 1.0
O A:ILE157 2.7 18.4 1.0
O A:ALA152 2.7 20.6 1.0
O A:VAL154 2.9 23.9 1.0
O A:LYS155 2.9 25.6 1.0
O A:HOH403 3.0 40.2 1.0
C A:LYS155 3.4 32.5 1.0
CA A:LYS155 3.6 34.2 1.0
C A:VAL154 3.7 26.8 1.0
C A:ILE157 3.7 19.4 1.0
C A:ALA152 3.8 16.9 1.0
N A:ILE157 4.1 20.6 1.0
N A:LYS155 4.2 31.9 1.0
N A:ASN156 4.4 25.7 1.0
CA A:ILE157 4.4 19.5 1.0
CA A:ALA152 4.5 20.5 1.0
O A:HOH444 4.5 30.3 1.0
CG2 A:ILE158 4.5 25.8 1.0
O A:HOH622 4.5 38.9 1.0
N A:VAL154 4.6 22.8 1.0
CD A:LYS155 4.7 48.4 1.0
N A:ILE158 4.7 17.1 1.0
CA A:ILE158 4.7 18.9 1.0
C A:LYS153 4.7 29.3 1.0
NZ A:LYS155 4.8 53.6 1.0
N A:LYS153 4.8 20.0 1.0
CA A:VAL154 4.8 20.1 1.0
C A:ASN156 4.8 21.9 1.0
CB A:ILE157 4.8 19.4 1.0
CA A:LYS153 4.9 23.5 1.0
CB A:LYS155 4.9 40.7 1.0
CA A:ASN156 5.0 22.9 1.0

Sodium binding site 4 out of 10 in 5t25

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Sodium binding site 4 out of 10 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:33.1
occ:1.00
 O A:HOH507 2.5 19.5 1.0
OD2 A:ASP265 3.0 25.3 1.0
N A:ILE274 3.0 13.7 1.0
O A:HOH627 3.0 21.6 1.0
O A:HOH405 3.4 37.3 1.0
CA A:PRO273 3.4 16.8 1.0
CG A:ASP265 3.4 18.2 1.0
CG2 A:ILE274 3.5 18.4 1.0
C A:PRO273 3.7 17.2 1.0
CB A:PRO273 3.8 16.4 1.0
CB A:ILE274 3.9 14.5 1.0
O A:ASP265 3.9 18.9 1.0
OD1 A:ASP265 4.0 19.5 1.0
CB A:ASP265 4.1 19.8 1.0
CA A:ILE274 4.1 14.6 1.0
O A:HOH596 4.3 33.2 1.0
O A:HOH542 4.3 35.7 1.0
CD1 A:LEU267 4.4 17.2 1.0
CG2 A:ILE250 4.6 13.0 1.0
O A:HOH706 4.7 43.1 1.0
N A:PRO273 4.7 16.9 1.0
CB A:TRP254 4.7 16.2 1.0
C A:ASP265 4.7 18.8 1.0
O A:ILE250 4.8 16.1 1.0
CG A:PRO273 4.8 18.4 1.0
O A:THR272 4.9 15.4 1.0
CD1 A:TRP254 4.9 16.3 1.0
O A:PRO273 5.0 14.8 1.0

Sodium binding site 5 out of 10 in 5t25

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Sodium binding site 5 out of 10 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:35.5
occ:1.00
 O A:HOH692 2.9 40.2 1.0
O A:HOH711 3.0 35.6 1.0
N A:ALA22 3.0 19.4 1.0
O A:HOH674 3.3 29.4 1.0
CB A:ALA22 3.3 21.7 1.0
N A:ARG21 3.5 18.8 1.0
CA A:ALA22 3.7 23.6 1.0
C A:ARG21 3.9 18.1 1.0
CA A:ARG21 4.0 19.7 1.0
CB A:ARG21 4.0 20.7 1.0
SG A:CYS20 4.1 23.4 1.0
C A:CYS20 4.2 17.8 1.0
CA A:CYS20 4.5 21.3 1.0
O A:HOH615 4.7 39.8 1.0
O A:HOH650 4.9 25.7 1.0
O A:HOH652 4.9 39.1 1.0
O A:HOH697 4.9 42.5 1.0
O A:CYS20 4.9 17.4 1.0
CB A:CYS20 5.0 18.6 1.0
C A:ALA22 5.0 21.4 1.0

Sodium binding site 6 out of 10 in 5t25

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Sodium binding site 6 out of 10 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:26.0
occ:1.00
 O B:HOH652 2.4 34.0 1.0
O B:ILE157 2.7 18.8 1.0
O B:ALA152 2.8 19.7 1.0
O B:VAL154 2.9 26.6 1.0
O B:HOH671 3.0 34.1 1.0
O B:LYS155 3.1 30.0 1.0
C B:ILE157 3.7 17.5 1.0
C B:LYS155 3.9 31.2 1.0
C B:ALA152 3.9 21.3 1.0
C B:VAL154 4.0 27.9 1.0
N B:ILE157 4.1 20.0 1.0
O B:HOH642 4.3 42.7 1.0
CA B:ILE157 4.4 18.4 1.0
CA B:LYS155 4.5 29.9 1.0
CA B:ALA152 4.5 18.9 1.0
O B:HOH564 4.5 34.0 1.0
N B:ILE158 4.6 17.2 1.0
CA B:ILE158 4.6 18.6 1.0
N B:ASN156 4.7 26.8 1.0
N B:VAL154 4.7 20.6 1.0
N B:LYS155 4.7 27.1 1.0
C B:LYS153 4.8 28.0 1.0
CB B:ILE157 4.8 18.8 1.0
C B:ASN156 4.8 23.1 1.0
CG2 B:ILE158 4.8 22.1 1.0
N B:LYS153 4.9 18.2 1.0

Sodium binding site 7 out of 10 in 5t25

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Sodium binding site 7 out of 10 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:27.0
occ:1.00
 N B:GLU146 2.9 14.9 1.0
O B:HOH416 3.1 35.5 1.0
CB B:GLU146 3.3 27.0 1.0
N B:PRO145 3.5 15.1 1.0
CD B:PRO145 3.5 12.4 1.0
CB B:LEU144 3.6 13.6 1.0
CA B:GLU146 3.7 16.9 1.0
CB B:PRO145 3.8 14.1 1.0
C B:PRO145 3.8 16.0 1.0
CA B:PRO145 3.9 13.8 1.0
C B:LEU144 4.0 13.3 1.0
CG B:PRO145 4.1 15.9 1.0
CA B:LEU144 4.4 12.4 1.0
CD1 B:LEU144 4.5 18.8 1.0
CG B:GLU146 4.6 36.1 1.0
CG B:LEU144 4.6 15.8 1.0
O B:LEU144 4.7 13.3 1.0
CD B:GLU146 4.8 44.6 1.0
OE1 B:GLU146 4.9 53.9 1.0
C B:GLU146 4.9 20.0 1.0

Sodium binding site 8 out of 10 in 5t25

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Sodium binding site 8 out of 10 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:27.5
occ:1.00
 O B:HOH711 2.5 31.3 1.0
O B:HOH683 2.8 34.7 1.0
N B:GLU113 2.9 15.8 1.0
O B:HOH594 3.1 21.9 1.0
N B:GLN112 3.4 15.0 1.0
CB B:GLN112 3.6 16.1 1.0
CB B:GLU113 3.6 16.5 1.0
CB B:SER111 3.7 15.6 1.0
CA B:GLN112 3.7 20.6 1.0
C B:GLN112 3.7 17.2 1.0
OG B:SER111 3.8 12.5 1.0
O B:HOH640 3.8 31.4 1.0
CA B:GLU113 3.8 16.3 1.0
O A:HOH690 4.1 36.5 1.0
C B:SER111 4.2 14.9 1.0
O B:HOH491 4.5 30.7 1.0
CA B:SER111 4.5 18.0 1.0
CG B:GLN112 4.5 18.2 1.0
O B:GLN112 4.9 15.1 1.0
O B:HOH720 5.0 29.4 1.0

Sodium binding site 9 out of 10 in 5t25

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Sodium binding site 9 out of 10 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:31.6
occ:1.00
 O B:HOH707 2.6 34.9 1.0
O B:PRO110 2.8 12.8 1.0
O B:HOH540 2.9 17.7 1.0
NE2 B:GLN112 3.1 15.2 1.0
CA B:SER111 3.6 18.0 1.0
C B:SER111 3.7 14.9 1.0
N B:GLN112 3.7 15.0 1.0
O B:HOH666 3.8 30.4 1.0
O B:HOH535 3.8 15.6 1.0
C B:PRO110 3.8 13.0 1.0
O B:HOH594 4.0 21.9 1.0
N B:SER111 4.2 14.2 1.0
CD B:GLN112 4.2 18.3 1.0
O B:HOH720 4.3 29.4 1.0
O B:SER111 4.4 13.3 1.0
CG B:GLN112 4.5 18.2 1.0
CA B:GLN112 4.7 20.6 1.0
CB B:CYS141 4.7 24.6 1.0
O B:ASP142 4.7 12.7 1.0
CB B:SER111 4.8 15.6 1.0
CD1 B:LEU115 4.9 13.4 1.0

Sodium binding site 10 out of 10 in 5t25

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Sodium binding site 10 out of 10 in the Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:32.2
occ:1.00
 N B:ALA22 2.9 22.4 1.0
O B:HOH689 3.2 27.7 1.0
CB B:ALA22 3.4 26.3 1.0
N B:ARG21 3.5 20.3 1.0
O B:HOH615 3.5 30.2 1.0
CA B:ALA22 3.7 19.5 1.0
C B:ARG21 3.9 18.0 1.0
CB B:ARG21 3.9 19.3 1.0
CA B:ARG21 3.9 21.1 1.0
SG B:CYS20 4.2 24.8 1.0
C B:CYS20 4.2 21.5 1.0
CA B:CYS20 4.6 21.2 1.0
O B:HOH573 4.8 36.6 1.0
O B:HOH677 4.9 21.5 1.0
C B:ALA22 5.0 19.4 1.0

Reference:

L.Chooback, L.M.Thomas, W.E.Karsten, C.D.Fleming, P.Seabourn. Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase From Escherichia Coli. To Be Published.
Page generated: Tue Oct 8 00:00:53 2024

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