Sodium in PDB 2ej6: Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound D-Proline

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

The structure of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound D-Proline, PDB code: 2ej6 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)	24.68 / 2.06
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	100.761, 100.761, 279.930, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 23.1

The binding sites of Sodium atom in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound D-Proline (pdb code 2ej6). 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 D-Proline, PDB code: 2ej6:
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 D-Proline


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 D-Proline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1540 b:31.9 occ:1.00 O A:HOH5578 2.4 25.1 1.0 O A:LEU56 2.6 21.5 1.0 O A:GLU123 2.9 19.3 1.0 O A:ASP211 2.9 23.1 1.0 OG A:SER55 2.9 26.2 1.0 CG A:GLU123 3.4 21.2 1.0 N A:LEU56 3.5 21.8 1.0 C A:LEU56 3.7 21.8 1.0 C A:ASP211 3.8 23.0 1.0 C A:GLU123 3.9 18.3 1.0 C A:SER55 4.1 24.3 1.0 CB A:SER55 4.1 24.7 1.0 CA A:ASP211 4.1 23.6 1.0 CA A:LEU56 4.1 21.3 1.0 CA A:SER55 4.2 24.7 1.0 OE1 A:GLU123 4.3 24.3 1.0 CA A:GLU123 4.3 19.3 1.0 CD A:GLU123 4.3 26.4 1.0 CB A:ASP211 4.4 22.6 1.0 CB A:GLU123 4.5 19.0 1.0 OD1 A:ASP211 4.7 27.6 1.0 CD A:PRO58 4.8 19.8 1.0 N A:ASN57 4.8 21.2 1.0 CB A:LEU56 4.9 21.0 1.0 N A:ALA212 4.9 21.8 1.0 O A:SER55 5.0 25.5 1.0

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


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 D-Proline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na5540 b:37.8 occ:1.00 O B:HOH5811 2.1 25.6 1.0 O B:LEU56 2.8 26.6 1.0 O B:ASP211 2.9 24.4 1.0 O B:GLU123 3.0 19.6 1.0 OG B:SER55 3.4 29.1 1.0 N B:LEU56 3.7 24.5 1.0 C B:ASP211 3.7 24.3 1.0 C B:LEU56 3.9 25.2 1.0 CG B:GLU123 3.9 21.7 1.0 CA B:ASP211 4.0 24.9 1.0 C B:GLU123 4.2 18.3 1.0 OD1 B:ASP211 4.2 33.9 1.0 CA B:LEU56 4.3 24.4 1.0 CB B:ASP211 4.3 25.1 1.0 C B:SER55 4.4 23.6 1.0 CB B:SER55 4.5 23.6 1.0 CA B:SER55 4.5 24.5 1.0 OE1 B:GLU123 4.6 24.5 1.0 CD B:PRO58 4.6 21.6 1.0 CA B:GLU123 4.7 17.6 1.0 CD B:GLU123 4.8 22.8 1.0 CG B:ASP211 4.8 29.2 1.0 O B:VAL364 4.9 20.6 1.0 N B:ALA212 4.9 22.7 1.0 CB B:LEU56 5.0 24.7 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.