Sodium in PDB 4r54: Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid

All present enzymatic activity of Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid:
1.2.1.11;

The structure of Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid, PDB code: 4r54 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 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.537, 98.806, 64.098, 90.00, 101.16, 90.00
R / Rfree (%)	18.4 / 21.9

The binding sites of Sodium atom in the Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid (pdb code 4r54). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid, PDB code: 4r54:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:30.0 occ:1.00 O A:PHE276 2.2 30.2 1.0 O A:ALA279 2.2 37.8 1.0 O A:ALA274 2.4 31.9 1.0 C A:PHE276 3.1 29.3 1.0 C A:ALA274 3.3 32.8 1.0 N A:PHE276 3.4 30.4 1.0 C A:ALA279 3.4 34.6 1.0 O A:ILE273 3.5 29.4 1.0 C A:ALA275 3.8 31.8 1.0 CA A:PHE276 3.9 30.4 1.0 O A:HOH615 3.9 43.4 1.0 N A:ALA279 4.0 32.5 1.0 CA A:ALA274 4.1 31.8 1.0 N A:PRO277 4.1 30.8 1.0 N A:ALA275 4.1 32.4 1.0 O A:HOH597 4.1 41.3 1.0 CA A:ALA279 4.1 34.2 1.0 CA A:PRO277 4.2 33.2 1.0 CA A:ALA275 4.2 33.8 1.0 CB A:ALA279 4.4 34.9 1.0 O A:ALA275 4.4 33.3 1.0 N A:GLY278 4.5 32.7 1.0 N A:VAL280 4.5 32.4 1.0 C A:ILE273 4.5 32.4 1.0 C A:PRO277 4.6 33.0 1.0 CB A:PHE276 4.7 31.6 1.0 CA A:VAL280 4.8 34.7 0.5 CA A:VAL280 4.8 34.7 0.5 N A:ALA274 4.8 30.9 1.0

Sodium binding site 2 out of 3 in the Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:31.3 occ:1.00 O A:GLU343 2.3 37.7 1.0 C A:GLU343 3.4 37.4 1.0 CA A:GLU343 4.2 36.5 1.0 N A:ARG344 4.2 37.8 1.0 CA A:ARG344 4.3 38.6 1.0 N A:GLY345 4.5 35.6 1.0 C A:ARG344 4.6 36.4 1.0 O A:HIS342 4.6 34.9 1.0

Sodium binding site 3 out of 3 in the Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Complex Crystal Structure of Sp-Aspartate-Semialdehyde-Dehydrogenase with 3-Carboxy-Ethyl-Phthalic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:47.0 occ:1.00 O B:HOH572 2.3 39.0 1.0 O B:HOH602 2.3 52.1 1.0 O B:SER236 2.4 40.2 1.0 OD1 B:ASP147 2.4 46.5 1.0 O B:HOH524 2.5 41.4 1.0 O B:ASP147 2.5 29.5 1.0 C B:ASP147 3.4 36.7 1.0 C B:SER236 3.5 38.9 1.0 CG B:ASP147 3.6 43.3 1.0 CA B:ASP147 3.6 36.9 1.0 N B:ALA238 4.1 31.6 1.0 CA B:ILE237 4.1 38.0 1.0 N B:ILE237 4.2 38.9 1.0 CB B:ASP147 4.2 38.8 1.0 NZ B:LYS261 4.3 59.7 1.0 OG B:SER236 4.3 41.8 1.0 CB B:SER236 4.4 39.5 1.0 CA B:SER236 4.5 39.5 1.0 C B:ILE237 4.6 32.8 1.0 OD2 B:ASP147 4.6 49.6 1.0 O B:LEU146 4.6 36.7 1.0 N B:ARG148 4.7 32.5 1.0 CB B:ALA238 4.8 32.8 1.0 N B:ASP147 4.8 37.7 1.0

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