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Sodium in PDB 3pzr: Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Vibrio Cholerae with Nadp and Product of S-Carbamoyl-L-Cysteine

Enzymatic activity of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Vibrio Cholerae with Nadp and Product of S-Carbamoyl-L-Cysteine

All present enzymatic activity of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Vibrio Cholerae with Nadp and Product of S-Carbamoyl-L-Cysteine:
1.2.1.11;

Protein crystallography data

The structure of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Vibrio Cholerae with Nadp and Product of S-Carbamoyl-L-Cysteine, PDB code: 3pzr was solved by A.G.Pavlovsky, N.Potente, R.E.Viola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.00 / 1.75
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 155.019, 155.019, 69.178, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Vibrio Cholerae with Nadp and Product of S-Carbamoyl-L-Cysteine (pdb code 3pzr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Vibrio Cholerae with Nadp and Product of S-Carbamoyl-L-Cysteine, PDB code: 3pzr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3pzr

Go back to Sodium Binding Sites List in 3pzr
Sodium binding site 1 out of 2 in the Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Vibrio Cholerae with Nadp and Product of S-Carbamoyl-L-Cysteine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Vibrio Cholerae with Nadp and Product of S-Carbamoyl-L-Cysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na373

b:19.4
occ:1.00
 O A:PHE212 2.3 11.1 1.0
O A:HOH437 2.3 11.3 1.0
O A:HOH441 2.4 11.2 1.0
OG1 A:THR214 2.5 11.3 1.0
O A:GLY210 2.9 12.6 1.0
C A:PHE212 3.5 10.9 1.0
CB A:THR214 3.6 11.4 1.0
N A:THR214 3.7 11.3 1.0
C A:GLY210 3.9 12.4 1.0
CG2 A:THR214 3.9 11.5 1.0
O A:HOH1000 4.0 27.0 1.0
CA A:THR214 4.2 11.4 1.0
N A:PHE212 4.3 11.5 1.0
O A:SER209 4.3 10.9 1.0
CA A:PHE212 4.4 10.8 1.0
C A:PRO213 4.5 10.9 1.0
CA A:GLY210 4.5 12.2 1.0
N A:PRO213 4.5 10.9 1.0
CA A:PRO213 4.6 11.0 1.0
O A:HOH590 4.6 25.7 1.0
CB A:PHE212 4.6 10.3 1.0
C A:SER211 4.7 12.1 1.0
C A:THR214 4.8 11.9 1.0
N A:SER211 4.9 12.6 1.0

Sodium binding site 2 out of 2 in 3pzr

Go back to Sodium Binding Sites List in 3pzr
Sodium binding site 2 out of 2 in the Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Vibrio Cholerae with Nadp and Product of S-Carbamoyl-L-Cysteine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystals Structure of Aspartate Beta-Semialdehyde Dehydrogenase From Vibrio Cholerae with Nadp and Product of S-Carbamoyl-L-Cysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na373

b:23.1
occ:1.00
 O B:HOH454 2.3 11.4 1.0
O B:HOH445 2.4 20.4 1.0
O B:HOH458 2.4 16.1 1.0
O B:HOH438 2.5 13.4 1.0
O B:GLY210 2.5 13.1 1.0
O B:PHE212 2.6 12.0 1.0
C B:PHE212 3.6 11.8 1.0
C B:GLY210 3.7 13.2 1.0
O B:HOH375 4.1 7.9 1.0
C B:SER211 4.1 12.8 1.0
N B:PHE212 4.2 12.1 1.0
N B:THR214 4.2 12.2 1.0
O B:HOH383 4.2 13.5 1.0
CA B:PRO213 4.3 11.9 1.0
OG1 B:THR214 4.3 12.7 1.0
N B:PRO213 4.4 11.7 1.0
O B:SER211 4.4 12.6 1.0
CA B:SER211 4.4 13.5 1.0
N B:SER211 4.5 13.4 1.0
CA B:PHE212 4.5 11.6 1.0
O B:HOH466 4.6 29.9 1.0
CA B:GLY210 4.7 13.1 1.0
C B:PRO213 4.8 11.9 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: Mon Oct 7 12:24:56 2024

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