Sodium in PDB 2ejd: Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine

All present enzymatic activity of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine:
1.5.1.12;

The structure of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine, PDB code: 2ejd was solved by E.Inagaki, K.Sakamoto, S.Yokoyama, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.51 / 1.85
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	101.661, 101.661, 279.261, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 19

The binding sites of Sodium atom in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine (pdb code 2ejd). 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 Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine, PDB code: 2ejd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1540 b:25.8 occ:1.00 O A:HOH2578 2.3 28.2 1.0 O A:LEU56 2.7 14.7 1.0 O A:GLU123 2.7 9.7 1.0 O A:ASP211 2.8 14.2 1.0 OG A:SER55 3.1 15.9 1.0 O A:HOH2790 3.2 28.3 1.0 CG A:GLU123 3.5 10.5 1.0 N A:LEU56 3.7 14.6 1.0 C A:LEU56 3.8 14.5 1.0 C A:GLU123 3.8 10.0 1.0 C A:ASP211 3.8 13.8 1.0 CA A:ASP211 4.2 14.2 1.0 C A:SER55 4.2 14.6 1.0 CA A:GLU123 4.2 9.1 1.0 CA A:LEU56 4.3 14.3 1.0 CB A:SER55 4.3 15.2 1.0 O A:HOH2857 4.4 30.1 1.0 CA A:SER55 4.4 15.2 1.0 OE1 A:GLU123 4.4 11.5 1.0 CB A:ASP211 4.4 14.1 1.0 CD A:GLU123 4.5 11.5 1.0 CB A:GLU123 4.5 9.2 1.0 CD A:PRO58 4.5 9.9 1.0 OD1 A:ASP211 4.6 19.9 1.0 N A:ASN57 4.9 13.5 1.0 N A:VAL124 4.9 8.6 1.0 N A:ALA212 4.9 11.9 1.0 CB A:LEU56 5.0 14.5 1.0

Sodium binding site 2 out of 2 in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2540 b:26.1 occ:1.00 O B:HOH2923 2.0 30.1 1.0 O B:HOH2788 2.3 24.7 1.0 O B:GLU123 2.4 14.5 1.0 O B:LEU56 2.7 17.4 1.0 O B:ASP211 2.9 17.0 1.0 OG B:SER55 3.5 20.3 1.0 CG B:GLU123 3.5 14.2 1.0 C B:GLU123 3.5 14.0 1.0 C B:LEU56 3.8 17.4 1.0 N B:LEU56 3.9 18.2 1.0 C B:ASP211 3.9 16.2 1.0 CA B:GLU123 4.1 14.1 1.0 O B:HOH2933 4.1 43.0 1.0 CD B:PRO58 4.2 13.6 1.0 CA B:ASP211 4.3 16.6 1.0 CB B:GLU123 4.4 13.8 1.0 CA B:LEU56 4.4 18.1 1.0 CB B:ASP211 4.5 17.0 1.0 OE1 B:GLU123 4.6 12.7 1.0 CD B:GLU123 4.6 16.2 1.0 C B:SER55 4.6 19.2 1.0 N B:VAL124 4.7 14.2 1.0 CB B:SER55 4.7 19.7 1.0 OD1 B:ASP211 4.7 20.8 1.0 CA B:SER55 4.8 19.5 1.0 O B:VAL364 4.8 14.0 1.0 N B:ASN57 4.9 16.0 1.0 CA B:VAL124 5.0 13.8 1.0 CG1 B:VAL124 5.0 13.8 1.0

E.Inagaki, N.Ohshima, K.Sakamoto, S.Yokoyama, T.H.Tahirov. Crystal Structure Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase in Ternary Complex with Inhibitor and Nad To Be Published.