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

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

The structure of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Proline, PDB code: 2eiw 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)	24.61 / 1.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	100.349, 100.349, 279.993, 90.00, 90.00, 120.00
R / Rfree (%)	15.7 / 19.2

The binding sites of Sodium atom in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Proline (pdb code 2eiw). 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-Proline, PDB code: 2eiw:
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-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 L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1540 b:24.7 occ:1.00 O A:HOH5703 2.5 26.3 1.0 O A:LEU56 2.6 16.4 1.0 O A:ASP211 2.7 14.7 1.0 O A:HOH5916 2.7 37.3 1.0 O A:GLU123 2.8 12.1 1.0 OG A:SER55 2.9 17.3 1.0 CG A:GLU123 3.5 15.0 1.0 N A:LEU56 3.6 15.4 1.0 C A:ASP211 3.7 15.4 1.0 C A:LEU56 3.7 15.5 1.0 C A:GLU123 3.8 12.0 1.0 CB A:SER55 4.1 17.8 1.0 C A:SER55 4.1 17.2 1.0 CA A:ASP211 4.1 16.1 1.0 CA A:SER55 4.2 17.1 1.0 CA A:GLU123 4.3 12.6 1.0 CA A:LEU56 4.3 15.7 1.0 CB A:ASP211 4.4 15.4 1.0 O A:HOH5708 4.4 24.7 1.0 OE1 A:GLU123 4.4 17.4 1.0 CD A:GLU123 4.5 17.0 1.0 CB A:GLU123 4.5 12.1 1.0 CD A:PRO58 4.7 14.9 1.0 OD1 A:ASP211 4.7 21.2 1.0 N A:ALA212 4.9 14.9 1.0 N A:ASN57 4.9 15.3 1.0 O A:SER55 4.9 17.2 1.0 N A:VAL124 5.0 11.6 1.0 CB A:LEU56 5.0 15.9 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-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 L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na5540 b:26.2 occ:1.00 O B:HOH5892 2.0 30.0 1.0 O B:HOH5893 2.3 10.7 0.5 O B:LEU56 2.5 17.1 1.0 O B:GLU123 2.5 14.9 1.0 O B:ASP211 3.0 16.2 1.0 OG B:SER55 3.4 19.5 1.0 CG B:GLU123 3.5 16.0 1.0 C B:LEU56 3.7 17.5 1.0 C B:GLU123 3.7 15.2 1.0 N B:LEU56 3.8 18.6 1.0 C B:ASP211 3.9 15.9 1.0 CA B:GLU123 4.2 14.9 1.0 CA B:ASP211 4.2 16.2 1.0 CA B:LEU56 4.3 18.2 1.0 CD B:PRO58 4.3 14.2 1.0 CB B:ASP211 4.4 15.8 1.0 CB B:GLU123 4.5 14.7 1.0 OD1 B:ASP211 4.6 21.2 1.0 C B:SER55 4.6 18.4 1.0 CD B:GLU123 4.6 17.6 1.0 OE1 B:GLU123 4.6 16.6 1.0 CB B:SER55 4.6 18.0 1.0 O B:HOH5755 4.6 30.3 1.0 CA B:SER55 4.8 18.3 1.0 O B:VAL364 4.8 13.7 1.0 N B:VAL124 4.8 14.7 1.0 N B:ASN57 4.8 15.8 1.0 CB B:LEU56 4.8 18.6 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.