Sodium in PDB 4r3w: Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex

All present enzymatic activity of Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex:
1.2.1.11;

The structure of Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex, PDB code: 4r3w 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)	62.76 / 1.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.964, 98.444, 64.263, 90.00, 102.43, 90.00
R / Rfree (%)	18.6 / 22.9

The binding sites of Sodium atom in the Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex (pdb code 4r3w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex, PDB code: 4r3w:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:33.6 occ:1.00 O A:ALA279 2.1 29.9 1.0 O A:PHE276 2.2 29.7 1.0 O A:ALA274 2.5 32.6 1.0 C A:PHE276 3.2 28.5 1.0 C A:ALA279 3.3 30.0 1.0 C A:ALA274 3.4 32.3 1.0 N A:PHE276 3.5 28.9 1.0 O A:ILE273 3.6 31.5 1.0 C A:ALA275 3.9 31.1 1.0 N A:ALA279 3.9 30.0 1.0 CA A:PHE276 4.0 28.8 1.0 CA A:ALA279 4.0 28.2 1.0 N A:PRO277 4.1 30.4 1.0 CA A:ALA274 4.2 34.9 1.0 N A:ALA275 4.2 32.1 1.0 CB A:ALA279 4.2 27.9 1.0 O A:HOH590 4.3 37.2 1.0 CA A:PRO277 4.3 31.0 1.0 N A:VAL280 4.4 28.2 1.0 CA A:ALA275 4.4 34.2 1.0 N A:GLY278 4.5 27.9 1.0 O A:ALA275 4.5 30.3 1.0 C A:ILE273 4.6 34.9 1.0 C A:PRO277 4.6 28.7 1.0 CA A:VAL280 4.7 28.5 1.0 CB A:PHE276 4.8 28.6 1.0 N A:ALA274 4.9 33.1 1.0 C A:GLY278 5.0 29.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:28.4 occ:1.00 O B:ALA279 2.2 25.3 1.0 O B:PHE276 2.2 28.6 1.0 O B:ALA274 2.4 32.9 1.0 O B:HOH573 2.5 33.4 1.0 C B:PHE276 3.1 29.8 1.0 C B:ALA274 3.3 34.0 1.0 O B:ILE273 3.4 28.7 1.0 C B:ALA279 3.4 26.5 1.0 N B:PHE276 3.4 29.4 1.0 C B:ALA275 3.8 30.6 1.0 CA B:PHE276 3.8 28.8 1.0 N B:ALA279 3.9 28.1 1.0 O B:HOH561 4.1 42.2 1.0 CA B:ALA279 4.1 28.1 1.0 N B:ALA275 4.1 32.5 1.0 CA B:ALA274 4.1 31.0 1.0 N B:PRO277 4.1 33.2 1.0 CB B:ALA279 4.3 28.0 1.0 O B:ALA275 4.3 29.1 1.0 CA B:ALA275 4.3 33.2 1.0 CA B:PRO277 4.3 32.1 1.0 N B:VAL280 4.4 26.1 1.0 C B:ILE273 4.4 28.5 1.0 N B:GLY278 4.5 31.0 1.0 CB B:PHE276 4.6 28.4 1.0 C B:PRO277 4.6 32.0 1.0 CA B:VAL280 4.7 26.7 1.0 N B:ALA274 4.8 29.2 1.0 C B:GLY278 5.0 28.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of the 1,2,3-Tricarboxylate Benzoic Acid Bound to Sp-Asadh-2'5'-Adp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:47.5 occ:1.00 O B:HOH574 2.3 42.8 1.0 O B:SER236 2.4 43.4 1.0 OD1 B:ASP147 2.5 50.6 1.0 O B:ASP147 2.6 33.8 1.0 C B:SER236 3.5 42.1 1.0 C B:ASP147 3.5 37.4 1.0 CG B:ASP147 3.6 47.5 1.0 CA B:ASP147 3.7 37.9 1.0 N B:ALA238 4.0 37.9 1.0 CA B:ILE237 4.2 39.3 1.0 N B:ILE237 4.3 40.2 1.0 CB B:ASP147 4.3 40.4 1.0 NZ B:LYS261 4.3 55.7 1.0 OG B:SER236 4.4 40.0 1.0 CB B:SER236 4.5 41.4 1.0 OD2 B:ASP147 4.5 53.9 1.0 CA B:SER236 4.5 41.9 1.0 C B:ILE237 4.6 38.4 1.0 CB B:ALA238 4.7 35.7 1.0 N B:ARG148 4.8 35.9 1.0 O B:LEU146 4.8 36.9 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