Atomistry » Sodium » PDB 4r3w-4rmj » 4r5h
Atomistry »
  Sodium »
    PDB 4r3w-4rmj »
      4r5h »

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: Sun Aug 17 21:34:59 2025

Last articles

Na in 6MKB
Na in 6ML1
Na in 6MLG
Na in 6MJQ
Na in 6MJI
Na in 6MJA
Na in 6MFM
Na in 6MIY
Na in 6MJ6
Na in 6MIV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy