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Sodium in PDB 4r5h: Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-Carboxy-Propenyl- Phthalic Acid

Enzymatic activity of Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-Carboxy-Propenyl- Phthalic Acid

All present enzymatic activity of Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-Carboxy-Propenyl- Phthalic Acid:
1.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-Carboxy-Propenyl- Phthalic Acid, PDB code: 4r5h was solved by A.G.Pavlovsky, B.Thangavelu, P.Bhansali, R.E.Viola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.50 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.620, 97.565, 64.555, 90.00, 100.39, 90.00
R / Rfree (%) 18.3 / 21.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-Carboxy-Propenyl- Phthalic Acid (pdb code 4r5h). 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 Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-Carboxy-Propenyl- Phthalic Acid, PDB code: 4r5h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4r5h

Go back to Sodium Binding Sites List in 4r5h
Sodium binding site 1 out of 2 in the Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-Carboxy-Propenyl- Phthalic Acid


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 Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-Carboxy-Propenyl- Phthalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:22.8
occ:1.00
 O A:PHE276 2.3 22.9 1.0
O A:ALA279 2.3 24.2 1.0
O A:ALA274 2.4 25.2 1.0
C A:PHE276 3.1 24.9 1.0
C A:ALA274 3.3 23.6 1.0
N A:PHE276 3.4 26.1 1.0
C A:ALA279 3.5 24.1 1.0
O A:HOH603 3.6 38.4 1.0
O A:ILE273 3.7 23.5 1.0
C A:ALA275 3.8 26.5 1.0
CA A:PHE276 3.8 24.2 1.0
N A:ALA279 4.0 20.5 1.0
N A:PRO277 4.1 24.6 1.0
N A:ALA275 4.1 25.2 1.0
CA A:ALA274 4.2 23.2 1.0
CA A:ALA279 4.2 21.2 1.0
CA A:ALA275 4.2 27.6 1.0
CA A:PRO277 4.3 24.6 1.0
O A:ALA275 4.3 24.7 1.0
O A:HOH621 4.3 36.8 1.0
N A:GLY278 4.5 21.9 1.0
CB A:ALA279 4.5 22.0 1.0
N A:VAL280 4.6 23.4 1.0
C A:PRO277 4.6 22.8 1.0
C A:ILE273 4.7 22.9 1.0
CB A:PHE276 4.7 25.1 1.0
CA A:VAL280 4.8 22.9 0.5
CA A:VAL280 4.8 22.9 0.5
N A:ALA274 4.9 23.6 1.0

Sodium binding site 2 out of 2 in 4r5h

Go back to Sodium Binding Sites List in 4r5h
Sodium binding site 2 out of 2 in the Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-Carboxy-Propenyl- Phthalic Acid


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 Sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-Carboxy-Propenyl- Phthalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:22.0
occ:1.00
 O A:GLU343 2.3 23.4 1.0
O A:HOH507 2.6 29.4 1.0
C A:GLU343 3.4 24.7 1.0
CA A:GLU343 4.3 24.8 1.0
N A:ARG344 4.3 25.2 1.0
N A:GLY345 4.4 23.7 1.0
O A:HIS342 4.5 20.6 1.0
CA A:ARG344 4.5 25.9 1.0
C A:ARG344 4.7 24.4 1.0

Reference:

A.G.Pavlovsky, B.Thangavelu, P.Bhansali, R.E.Viola. A Cautionary Tale of Structure-Guided Inhibitor Development Against An Essential Enzyme in the Aspartate-Biosynthetic Pathway Acta Crystallogr.,Sect.D V. 70 3244 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714023979
Page generated: Mon Oct 7 18:12:10 2024

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