Fluorine in PDB 7va1: Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35

All present enzymatic activity of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35:
1.1.1.37; 1.1.1.399; 1.1.1.95;

The structure of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35, PDB code: 7va1 was solved by Y.Cen, D.Gao, J.Zhou, P.Tian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.37 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.41, 112.52, 87.52, 90, 92.36, 90
R / Rfree (%)	19.6 / 22.5

The binding sites of Fluorine atom in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35 (pdb code 7va1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35, PDB code: 7va1:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:45.0 occ:1.00 F1 B:5YP401 0.0 45.0 1.0 C6 B:5YP401 1.3 39.4 1.0 C1 B:5YP401 2.4 33.4 1.0 C5 B:5YP401 2.4 34.4 1.0 CB B:LEU151 3.3 26.5 1.0 O B:TYR174 3.4 25.7 1.0 CA B:LEU151 3.6 31.4 1.0 C2 B:5YP401 3.6 28.6 1.0 CD2 B:TYR174 3.6 34.4 1.0 C4 B:5YP401 3.7 30.4 1.0 N B:GLY152 3.7 25.1 1.0 C B:LEU151 3.8 31.4 1.0 CD2 B:LEU151 3.9 29.4 1.0 CD2 B:LEU216 4.0 28.2 1.0 CG B:LEU151 4.0 28.7 1.0 C B:TYR174 4.1 23.5 1.0 C3 B:5YP401 4.1 31.5 1.0 CB B:TYR174 4.1 27.0 1.0 CD2 B:LEU193 4.2 29.9 1.0 CG2 B:THR207 4.3 30.4 1.0 CG B:TYR174 4.4 29.5 1.0 CD1 B:LEU151 4.4 27.5 1.0 O B:LEU151 4.6 28.2 1.0 CE2 B:TYR174 4.6 37.9 1.0 CA B:TYR174 4.7 27.6 1.0 CA B:GLY152 4.7 22.5 1.0 CG B:LEU193 4.7 35.2 1.0 CD1 B:LEU193 4.8 33.2 1.0 N B:ASP175 4.8 27.3 1.0 C7 B:5YP401 4.8 26.0 1.0 CD1 B:LEU216 4.9 34.6 1.0 CG B:LEU216 5.0 29.2 1.0 CA B:ASP175 5.0 28.8 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:44.8 occ:1.00 F1 A:5YP401 0.0 44.8 1.0 C6 A:5YP401 1.3 42.5 1.0 C1 A:5YP401 2.3 40.5 1.0 C5 A:5YP401 2.4 43.2 1.0 CD2 A:TYR174 3.2 34.0 1.0 O A:TYR174 3.4 29.9 1.0 CB A:LEU151 3.4 31.1 1.0 CA A:LEU151 3.6 28.3 1.0 C2 A:5YP401 3.6 45.8 1.0 C4 A:5YP401 3.6 49.5 1.0 N A:GLY152 3.7 27.6 1.0 C A:LEU151 3.8 28.9 1.0 CD2 A:LEU151 4.0 32.3 1.0 CB A:TYR174 4.0 29.5 1.0 C A:TYR174 4.0 30.4 1.0 CG A:TYR174 4.1 32.5 1.0 CD2 A:LEU216 4.1 43.7 1.0 C3 A:5YP401 4.1 47.6 1.0 CE2 A:TYR174 4.1 36.9 1.0 CG A:LEU151 4.1 32.5 1.0 CD1 A:LEU193 4.1 40.4 1.0 CG2 A:THR207 4.2 41.2 1.0 O A:LEU151 4.6 30.5 1.0 CD1 A:LEU151 4.6 33.7 1.0 CA A:TYR174 4.6 30.1 1.0 CA A:GLY152 4.7 27.5 1.0 N A:ASP175 4.8 29.5 1.0 C7 A:5YP401 4.8 46.0 1.0 CD2 A:LEU193 5.0 49.5 1.0 CA A:ASP175 5.0 29.6 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35 within 5.0Å range: probe atom residue distance (Å) B Occ C:F401 b:45.0 occ:1.00 F1 C:5YP401 0.0 45.0 1.0 C6 C:5YP401 1.3 43.6 1.0 C1 C:5YP401 2.4 44.9 1.0 C5 C:5YP401 2.4 42.0 1.0 CB C:LEU151 3.4 26.5 1.0 O C:TYR174 3.5 30.3 1.0 CD2 C:TYR174 3.5 36.5 1.0 CA C:LEU151 3.6 25.1 1.0 C2 C:5YP401 3.6 43.6 1.0 N C:GLY152 3.6 27.1 1.0 C4 C:5YP401 3.6 37.5 1.0 C C:LEU151 3.8 28.3 1.0 CD2 C:LEU151 4.0 27.3 1.0 CG2 C:THR207 4.1 34.6 1.0 CD2 C:LEU216 4.1 40.6 1.0 C3 C:5YP401 4.1 38.7 1.0 C C:TYR174 4.1 30.2 1.0 CD1 C:LEU193 4.2 35.6 1.0 CG C:LEU151 4.2 27.5 1.0 CB C:TYR174 4.2 29.9 1.0 CG C:TYR174 4.4 36.7 1.0 CE2 C:TYR174 4.4 43.1 1.0 O C:LEU151 4.6 30.0 1.0 CD1 C:LEU151 4.6 30.0 1.0 CA C:GLY152 4.6 25.4 1.0 CA C:TYR174 4.8 29.6 1.0 C7 C:5YP401 4.9 42.0 1.0 N C:ASP175 4.9 23.9 1.0 CD2 C:LEU193 4.9 40.4 1.0 CA C:ASP175 5.0 25.0 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35 within 5.0Å range: probe atom residue distance (Å) B Occ D:F401 b:41.9 occ:1.00 F1 D:5YP401 0.0 41.9 1.0 C6 D:5YP401 1.3 33.2 1.0 C1 D:5YP401 2.4 30.3 1.0 C5 D:5YP401 2.4 31.0 1.0 CB D:LEU151 3.3 28.2 1.0 O D:TYR174 3.3 26.7 1.0 CA D:LEU151 3.5 30.2 1.0 C2 D:5YP401 3.6 34.0 1.0 N D:GLY152 3.6 28.6 1.0 C4 D:5YP401 3.7 36.6 1.0 CD2 D:TYR174 3.7 34.9 1.0 C D:LEU151 3.7 31.3 1.0 CD2 D:LEU151 3.8 26.7 1.0 CG D:LEU151 4.0 27.7 1.0 CD2 D:LEU216 4.0 32.2 1.0 C D:TYR174 4.0 26.9 1.0 CB D:TYR174 4.1 30.4 1.0 C3 D:5YP401 4.1 37.7 1.0 CD2 D:LEU193 4.2 29.6 1.0 CG2 D:THR207 4.3 32.3 1.0 CG D:TYR174 4.4 29.1 1.0 CD1 D:LEU151 4.4 28.7 1.0 O D:LEU151 4.5 25.8 1.0 CA D:TYR174 4.6 36.1 1.0 CE2 D:TYR174 4.6 39.3 1.0 CA D:GLY152 4.6 26.1 1.0 N D:ASP175 4.8 29.7 1.0 CG D:LEU193 4.8 32.2 1.0 CD1 D:LEU193 4.8 36.0 1.0 C7 D:5YP401 4.8 36.2 1.0 CD1 D:LEU216 4.9 39.7 1.0 N D:LEU151 5.0 25.6 1.0 CA D:ASP175 5.0 28.1 1.0 CG D:LEU216 5.0 34.6 1.0

Y.Cen, D.Gao, J.Zhou, P.Tian. Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with Gdd-04-35 To Be Published.