Sodium in PDB 2ehu: Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine

All present enzymatic activity of Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine:
1.5.1.12;

The structure of Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine, PDB code: 2ehu 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)	30.00 / 1.80
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	102.556, 102.556, 278.585, 90.00, 90.00, 120.00
R / Rfree (%)	13.9 / 16.7

The binding sites of Sodium atom in the Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine (pdb code 2ehu). 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 Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine, PDB code: 2ehu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine


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 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1540 b:20.3 occ:1.00 O A:HOH2729 2.3 25.2 1.0 O A:HOH2809 2.4 31.0 1.0 O A:LEU56 2.6 12.2 1.0 O A:GLU123 2.7 9.2 1.0 O A:ASP211 2.9 12.7 1.0 OG A:SER55 3.0 13.4 1.0 CG A:GLU123 3.5 9.2 1.0 N A:LEU56 3.6 12.0 1.0 C A:LEU56 3.7 11.6 1.0 C A:GLU123 3.8 9.7 1.0 C A:ASP211 3.8 11.7 1.0 C A:SER55 4.1 12.3 1.0 CA A:ASP211 4.2 12.2 1.0 CA A:LEU56 4.2 11.7 1.0 O A:HOH2725 4.2 25.3 1.0 CB A:SER55 4.2 12.8 1.0 CA A:GLU123 4.2 8.9 1.0 CA A:SER55 4.3 12.4 1.0 CB A:ASP211 4.4 12.4 1.0 CD A:PRO58 4.4 9.9 1.0 OE1 A:GLU123 4.5 9.1 1.0 CD A:GLU123 4.5 10.2 1.0 CB A:GLU123 4.5 8.9 1.0 OD1 A:ASP211 4.7 18.1 1.0 N A:ASN57 4.8 10.5 1.0 CB A:LEU56 4.9 12.1 1.0 O A:SER55 4.9 12.9 1.0 N A:VAL124 4.9 8.5 1.0 N A:ALA212 5.0 11.0 1.0 O A:VAL364 5.0 9.8 1.0

Sodium binding site 2 out of 3 in the Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine


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 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2540 b:5.3 occ:0.50 NA B:NA2540 0.0 5.3 0.5 NA B:NA2540 1.3 16.1 0.5 O B:GLU123 2.3 9.8 1.0 O B:HOH2794 2.3 28.8 1.0 O B:LEU56 2.4 12.7 1.0 O B:HOH2907 3.0 30.4 1.0 O B:ASP211 3.2 12.4 1.0 C B:GLU123 3.4 9.7 1.0 OG B:SER55 3.5 14.4 1.0 C B:LEU56 3.5 12.6 1.0 CG B:GLU123 3.6 9.3 1.0 N B:LEU56 3.7 12.6 1.0 CD B:PRO58 4.0 11.2 1.0 CA B:GLU123 4.0 9.2 1.0 O B:HOH2861 4.1 31.9 1.0 CA B:LEU56 4.2 12.8 1.0 C B:ASP211 4.3 11.4 1.0 CB B:GLU123 4.4 9.5 1.0 N B:VAL124 4.5 9.7 1.0 C B:SER55 4.5 13.2 1.0 N B:ASN57 4.6 11.5 1.0 CA B:ASP211 4.6 11.8 1.0 O B:VAL364 4.7 11.0 1.0 CB B:SER55 4.7 13.9 1.0 CD B:GLU123 4.7 12.2 1.0 CB B:ASP211 4.7 12.6 1.0 N B:PRO58 4.7 10.5 1.0 CA B:SER55 4.8 13.0 1.0 OE1 B:GLU123 4.8 10.5 1.0 CA B:VAL124 4.8 9.7 1.0 CG B:PRO58 4.8 10.8 1.0 OD1 B:ASP211 4.8 18.5 1.0 CB B:LEU56 4.8 13.1 1.0 CG1 B:VAL124 4.9 10.6 1.0 CA B:ASN57 4.9 11.1 1.0

Sodium binding site 3 out of 3 in the Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad and Inhibitor L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2540 b:16.1 occ:0.50 NA B:NA2540 0.0 16.1 0.5 NA B:NA2540 1.3 5.3 0.5 O B:HOH2907 2.3 30.4 1.0 OG B:SER55 2.6 14.4 1.0 O B:ASP211 2.7 12.4 1.0 O B:HOH2794 2.7 28.8 1.0 O B:LEU56 3.1 12.7 1.0 N B:LEU56 3.4 12.6 1.0 O B:GLU123 3.4 9.8 1.0 C B:ASP211 3.5 11.4 1.0 CG B:GLU123 3.7 9.3 1.0 CB B:SER55 3.7 13.9 1.0 CA B:ASP211 3.8 11.8 1.0 CA B:SER55 3.8 13.0 1.0 C B:SER55 4.0 13.2 1.0 C B:LEU56 4.0 12.6 1.0 OE1 B:GLU123 4.2 10.5 1.0 CB B:ASP211 4.2 12.6 1.0 CA B:LEU56 4.3 12.8 1.0 OD1 B:ASP211 4.3 18.5 1.0 O B:HOH2861 4.4 31.9 1.0 C B:GLU123 4.4 9.7 1.0 CD B:GLU123 4.4 12.2 1.0 N B:ALA212 4.6 10.5 1.0 CA B:GLU123 4.8 9.2 1.0 CG B:ASP211 4.8 15.5 1.0 CB B:GLU123 4.9 9.5 1.0 CB B:LEU56 4.9 13.1 1.0 O B:GLU210 4.9 10.9 1.0 O B:SER55 5.0 13.2 1.0

E.Inagaki, N.Ohshima. Crystal Structure Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase in Ternary Complex with Inhibitor and Nad. To Be Published.