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Sodium in PDB 3hij: Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate

Protein crystallography data

The structure of Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate, PDB code: 3hij was solved by J.E.Voss, S.W.Scally, R.C.J.Dobson, M.A.Perugini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.27 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.484, 124.617, 130.979, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 21

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate (pdb code 3hij). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate, PDB code: 3hij:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3hij

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Sodium binding site 1 out of 4 in the Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na294

b:20.5
occ:1.00
 O A:ILE176 2.3 16.3 1.0
O A:ALA180 2.3 22.9 1.0
O A:HOH336 2.3 15.4 1.0
OG1 A:THR179 2.4 14.9 1.0
O A:HOH298 2.4 20.5 1.0
O A:THR179 2.5 18.7 1.0
C A:THR179 3.1 19.9 1.0
C A:ALA180 3.2 24.7 1.0
O A:HOH393 3.2 21.0 1.0
C A:ILE176 3.3 16.7 1.0
CB A:THR179 3.5 19.1 1.0
CA A:THR179 3.8 19.0 1.0
CA A:ILE176 3.8 14.7 1.0
N A:ALA180 3.8 21.5 1.0
O A:HOH578 3.9 28.8 1.0
N A:THR179 4.0 18.0 1.0
N A:ASP181 4.0 25.1 1.0
O A:ILE175 4.1 14.9 1.0
CA A:ALA180 4.1 22.9 1.0
CA A:ASP181 4.1 25.5 1.0
O A:PHE183 4.2 19.5 1.0
CG2 A:ILE176 4.4 10.2 1.0
N A:GLU177 4.5 18.0 1.0
CB A:PHE183 4.7 17.3 1.0
CB A:ILE176 4.7 14.6 1.0
OD1 A:ASP181 4.7 28.8 1.0
C A:ASP181 4.7 25.8 1.0
C A:GLU177 4.8 19.8 1.0
O A:GLU177 4.8 18.3 1.0
N A:ILE176 4.9 15.9 1.0
CG2 A:THR179 4.9 16.4 1.0
C A:ILE175 4.9 15.4 1.0
CA A:GLU177 4.9 20.7 1.0

Sodium binding site 2 out of 4 in 3hij

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Sodium binding site 2 out of 4 in the Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na295

b:24.1
occ:1.00
 O B:THR179 2.4 21.5 1.0
OG1 B:THR179 2.4 15.8 1.0
O B:ALA180 2.4 22.2 1.0
O B:HOH386 2.5 20.6 1.0
O B:ILE176 2.5 18.8 1.0
O B:HOH355 2.6 25.5 1.0
C B:THR179 3.0 21.0 1.0
C B:ALA180 3.2 23.6 1.0
O B:HOH660 3.5 26.8 1.0
CB B:THR179 3.5 18.7 1.0
C B:ILE176 3.5 17.9 1.0
CA B:THR179 3.7 19.5 1.0
N B:ALA180 3.8 22.2 1.0
CA B:ILE176 3.9 17.1 1.0
N B:THR179 3.9 19.8 1.0
N B:ASP181 4.0 23.8 1.0
CA B:ALA180 4.1 23.0 1.0
O B:PHE183 4.1 18.0 1.0
CA B:ASP181 4.2 26.3 1.0
O B:ILE175 4.2 16.0 1.0
O B:HOH1048 4.4 34.9 1.0
CG2 B:ILE176 4.4 17.4 1.0
CB B:PHE183 4.5 18.5 1.0
O B:HOH632 4.7 28.4 1.0
N B:GLU177 4.7 20.4 1.0
OD2 B:ASP181 4.8 32.8 1.0
C B:ASP181 4.8 25.9 1.0
CB B:ILE176 4.8 16.9 1.0
CG2 B:THR179 4.8 15.5 1.0
O B:GLU177 4.8 21.6 1.0
N B:PHE183 4.9 22.6 1.0
C B:GLU177 4.9 21.6 1.0
O B:HOH1160 4.9 42.1 1.0
N B:ILE176 4.9 14.3 1.0
C B:ILE175 5.0 14.9 1.0

Sodium binding site 3 out of 4 in 3hij

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Sodium binding site 3 out of 4 in the Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na293

b:24.0
occ:1.00
 O C:HOH366 2.2 20.5 1.0
O C:HOH323 2.3 24.2 1.0
O C:ALA180 2.4 26.0 1.0
O C:THR179 2.5 23.2 1.0
OG1 C:THR179 2.6 19.8 1.0
O C:ILE176 2.6 19.4 1.0
C C:THR179 3.1 22.5 1.0
C C:ALA180 3.2 26.5 1.0
O C:HOH919 3.2 34.5 1.0
C C:ILE176 3.6 19.1 1.0
CB C:THR179 3.6 21.1 1.0
CA C:THR179 3.8 21.3 1.0
N C:ALA180 3.8 23.9 1.0
CA C:ILE176 4.0 16.6 1.0
N C:ASP181 4.0 27.7 1.0
N C:THR179 4.1 21.4 1.0
CA C:ALA180 4.1 25.2 1.0
O C:PHE183 4.1 22.4 1.0
CA C:ASP181 4.2 29.6 1.0
O C:ILE175 4.2 13.8 1.0
CG2 C:ILE176 4.4 14.1 1.0
OD1 C:ASP181 4.7 36.3 1.0
CB C:PHE183 4.7 21.1 1.0
N C:GLU177 4.8 19.6 1.0
CB C:ILE176 4.8 15.9 1.0
C C:ASP181 4.8 29.9 1.0
CG2 C:THR179 4.9 17.2 1.0
O C:GLU177 4.9 21.3 1.0
C C:GLU177 5.0 22.1 1.0
O C:HOH1067 5.0 35.4 1.0

Sodium binding site 4 out of 4 in 3hij

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Sodium binding site 4 out of 4 in the Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Dihydrodipicolinate Synthase From Bacillus Anthracis in Complex with Its Substrate, Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na294

b:20.0
occ:1.00
 O D:HOH348 2.1 20.3 1.0
O D:HOH425 2.3 25.0 1.0
O D:ILE176 2.4 23.2 1.0
O D:THR179 2.4 20.6 1.0
OG1 D:THR179 2.5 16.1 1.0
O D:ALA180 2.7 24.9 1.0
C D:THR179 3.0 21.9 1.0
C D:ALA180 3.4 25.5 1.0
C D:ILE176 3.4 21.0 1.0
CB D:THR179 3.5 18.7 1.0
CA D:THR179 3.7 20.5 1.0
CA D:ILE176 3.8 18.9 1.0
N D:ALA180 3.8 23.4 1.0
N D:THR179 3.9 21.2 1.0
N D:ASP181 4.0 26.6 1.0
O D:ILE175 4.1 17.6 1.0
CA D:ASP181 4.1 28.8 1.0
CA D:ALA180 4.2 24.4 1.0
O D:PHE183 4.2 21.6 1.0
CG2 D:ILE176 4.5 17.8 1.0
N D:GLU177 4.6 21.3 1.0
CB D:PHE183 4.7 19.7 1.0
OD1 D:ASP181 4.7 31.9 1.0
CB D:ILE176 4.7 18.3 1.0
C D:ASP181 4.8 29.1 1.0
C D:GLU177 4.8 22.6 1.0
CG2 D:THR179 4.8 16.6 1.0
N D:ILE176 4.8 17.5 1.0
O D:HOH863 4.8 34.4 1.0
C D:ILE175 4.9 17.0 1.0
N D:PHE183 5.0 24.8 1.0
CA D:GLU177 5.0 23.1 1.0
O D:GLU177 5.0 21.1 1.0

Reference:

J.E.Voss, S.W.Scally, N.L.Taylor, S.C.Atkinson, M.D.Griffin, C.A.Hutton, M.W.Parker, M.R.Alderton, J.A.Gerrard, R.C.Dobson, C.Dogovski, M.A.Perugini. Substrate-Mediated Stabilization of A Tetrameric Drug Target Reveals Achilles Heel in Anthrax. J.Biol.Chem. V. 285 5188 2010.
ISSN: ISSN 0021-9258
PubMed: 19948665
DOI: 10.1074/JBC.M109.038166
Page generated: Mon Oct 7 10:23:49 2024

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