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Sodium in PDB 3pwk: Crystal Structure of Aspartate Beta-Semialdehide Dehydrogenase From Streptococcus Pneumoniae with 2',5'-Adenosine Diphosphate and D-2- Aminoadipate

Enzymatic activity of Crystal Structure of Aspartate Beta-Semialdehide Dehydrogenase From Streptococcus Pneumoniae with 2',5'-Adenosine Diphosphate and D-2- Aminoadipate

All present enzymatic activity of Crystal Structure of Aspartate Beta-Semialdehide Dehydrogenase From Streptococcus Pneumoniae with 2',5'-Adenosine Diphosphate and D-2- Aminoadipate:
1.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Aspartate Beta-Semialdehide Dehydrogenase From Streptococcus Pneumoniae with 2',5'-Adenosine Diphosphate and D-2- Aminoadipate, PDB code: 3pwk was solved by A.G.Pavlovsky, R.E.Viola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.872, 99.660, 64.436, 90.00, 100.91, 90.00
R / Rfree (%) 13 / 16

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Aspartate Beta-Semialdehide Dehydrogenase From Streptococcus Pneumoniae with 2',5'-Adenosine Diphosphate and D-2- Aminoadipate (pdb code 3pwk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Aspartate Beta-Semialdehide Dehydrogenase From Streptococcus Pneumoniae with 2',5'-Adenosine Diphosphate and D-2- Aminoadipate, PDB code: 3pwk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3pwk

Go back to Sodium Binding Sites List in 3pwk
Sodium binding site 1 out of 2 in the Crystal Structure of Aspartate Beta-Semialdehide Dehydrogenase From Streptococcus Pneumoniae with 2',5'-Adenosine Diphosphate and D-2- Aminoadipate


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 Aspartate Beta-Semialdehide Dehydrogenase From Streptococcus Pneumoniae with 2',5'-Adenosine Diphosphate and D-2- Aminoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na373

b:10.8
occ:1.00
 O A:ALA279 2.3 11.6 1.0
O A:PHE276 2.3 10.0 1.0
O A:ALA274 2.4 11.0 1.0
C A:PHE276 3.2 9.8 1.0
C A:ALA274 3.3 10.9 1.0
N A:PHE276 3.4 10.0 1.0
C A:ALA279 3.4 10.0 1.0
O A:ILE273 3.7 10.3 1.0
C A:ALA275 3.7 10.6 1.0
CA A:PHE276 3.9 9.3 1.0
N A:ALA279 3.9 10.1 1.0
O A:HOH568 4.0 20.8 1.0
N A:PRO277 4.1 10.1 1.0
N A:ALA275 4.1 11.0 1.0
CA A:ALA279 4.1 9.7 1.0
CA A:ALA275 4.2 11.1 1.0
CA A:ALA274 4.2 11.0 1.0
O A:ALA275 4.2 11.8 1.0
CA A:PRO277 4.3 10.2 1.0
O A:HOH496 4.3 19.9 1.0
CB A:ALA279 4.4 10.8 1.0
N A:GLY278 4.5 10.3 1.0
N A:VAL280 4.5 9.8 1.0
C A:PRO277 4.6 10.7 1.0
C A:ILE273 4.7 10.3 1.0
CA A:VAL280 4.7 10.0 1.0
CB A:PHE276 4.7 9.8 1.0
C A:GLY278 5.0 9.8 1.0

Sodium binding site 2 out of 2 in 3pwk

Go back to Sodium Binding Sites List in 3pwk
Sodium binding site 2 out of 2 in the Crystal Structure of Aspartate Beta-Semialdehide Dehydrogenase From Streptococcus Pneumoniae with 2',5'-Adenosine Diphosphate and D-2- Aminoadipate


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 Aspartate Beta-Semialdehide Dehydrogenase From Streptococcus Pneumoniae with 2',5'-Adenosine Diphosphate and D-2- Aminoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na373

b:21.3
occ:1.00
 O B:HOH914 2.2 25.8 1.0
O B:HOH939 2.4 26.7 1.0
OD2 B:ASP147 2.5 20.3 1.0
O B:SER236 2.5 17.1 1.0
O B:HOH474 2.5 22.0 1.0
O B:ASP147 2.6 12.3 1.0
C B:ASP147 3.4 12.2 1.0
CG B:ASP147 3.4 18.4 1.0
C B:SER236 3.5 16.1 1.0
CA B:ASP147 3.6 12.9 1.0
O B:HOH377 3.9 47.1 1.0
N B:ALA238 4.0 11.9 1.0
CA B:ILE237 4.0 13.9 1.0
CB B:ASP147 4.1 14.4 1.0
N B:ILE237 4.2 14.7 1.0
OG B:SER236 4.2 17.4 1.0
OD1 B:ASP147 4.3 25.3 1.0
CB B:SER236 4.5 16.8 1.0
C B:ILE237 4.5 13.4 1.0
O B:LEU146 4.5 14.9 1.0
CA B:SER236 4.6 16.8 1.0
N B:ARG148 4.7 10.9 1.0
O B:HOH577 4.7 37.6 1.0
N B:ASP147 4.8 12.6 1.0
CB B:ALA238 4.8 12.1 1.0

Reference:

A.G.Pavlovsky, X.Liu, C.R.Faehnle, N.Potente, R.E.Viola. Structural Characterization of Inhibitors with Selectivity Against Members of A Homologous Enzyme Family. Chem.Biol.Drug Des. V. 79 128 2012.
ISSN: ISSN 1747-0277
PubMed: 22039970
DOI: 10.1111/J.1747-0285.2011.01267.X
Page generated: Tue Dec 15 06:22:00 2020

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