Sodium in PDB 2j5n: 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus with Bound Inhibitor Glycine and Nad.

All present enzymatic activity of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus with Bound Inhibitor Glycine and Nad.:
1.5.1.12;

The structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus with Bound Inhibitor Glycine and Nad., PDB code: 2j5n was solved by E.Inagaki, K.Sakamoto, M.Nishio, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.85 / 1.63
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	102.589, 102.589, 278.637, 90.00, 90.00, 120.00
R / Rfree (%)	14.6 / 17.4

The binding sites of Sodium atom in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus with Bound Inhibitor Glycine and Nad. (pdb code 2j5n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus with Bound Inhibitor Glycine and Nad., PDB code: 2j5n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus with Bound Inhibitor Glycine and Nad.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus with Bound Inhibitor Glycine and Nad. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1525 b:18.3 occ:1.00 O A:HOH2426 2.5 28.2 1.0 O A:HOH2143 2.5 25.7 1.0 O A:LEU56 2.6 11.9 1.0 O A:GLU123 2.7 7.7 1.0 O A:ASP211 2.8 11.7 1.0 OG A:SER55 3.0 12.1 1.0 CG A:GLU123 3.5 8.6 1.0 N A:LEU56 3.6 11.3 1.0 C A:LEU56 3.7 11.1 1.0 C A:GLU123 3.8 8.1 1.0 C A:ASP211 3.8 10.8 1.0 C A:SER55 4.1 11.8 1.0 CB A:SER55 4.2 12.2 1.0 CA A:LEU56 4.2 11.3 1.0 CA A:ASP211 4.2 11.3 1.0 CA A:GLU123 4.3 7.6 1.0 CA A:SER55 4.3 11.8 1.0 O A:HOH2425 4.3 21.5 1.0 OE1 A:GLU123 4.5 8.6 1.0 CD A:PRO58 4.5 10.0 1.0 CB A:ASP211 4.5 11.9 1.0 CD A:GLU123 4.5 9.0 1.0 CB A:GLU123 4.5 7.5 1.0 OD1 A:ASP211 4.7 18.2 1.0 N A:ASN57 4.8 10.7 1.0 N A:VAL124 4.9 7.7 1.0 CB A:LEU56 4.9 11.5 1.0 N A:ALA212 5.0 9.9 1.0 O A:SER55 5.0 12.6 1.0

Sodium binding site 2 out of 2 in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus with Bound Inhibitor Glycine and Nad.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophirus with Bound Inhibitor Glycine and Nad. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1526 b:18.5 occ:1.00 O B:HOH2420 2.4 28.0 1.0 O B:GLU123 2.5 9.3 1.0 O B:LEU56 2.5 10.9 1.0 O B:HOH2132 2.8 24.7 1.0 O B:ASP211 3.0 11.5 1.0 OG B:SER55 3.2 11.9 1.0 CG B:GLU123 3.6 10.3 1.0 C B:GLU123 3.6 8.9 1.0 C B:LEU56 3.6 11.7 1.0 N B:LEU56 3.7 11.6 1.0 C B:ASP211 4.0 10.8 1.0 CA B:GLU123 4.1 8.9 1.0 CA B:LEU56 4.2 11.7 1.0 CD B:PRO58 4.3 10.4 1.0 O B:HOH2421 4.3 30.4 1.0 CA B:ASP211 4.4 11.3 1.0 C B:SER55 4.4 11.9 1.0 CB B:SER55 4.5 12.6 1.0 CB B:GLU123 4.5 9.4 1.0 CA B:SER55 4.6 11.8 1.0 CB B:ASP211 4.6 12.2 1.0 CD B:GLU123 4.6 10.7 1.0 OE1 B:GLU123 4.6 10.6 1.0 OD1 B:ASP211 4.7 19.8 1.0 N B:VAL124 4.7 8.2 1.0 N B:ASN57 4.8 10.4 1.0 O B:VAL364 4.8 10.2 1.0 CB B:LEU56 4.9 12.3 1.0 CG1 B:VAL124 5.0 8.2 1.0 CG2 B:VAL65 5.0 15.2 1.0

E.Inagaki, K.Sakamoto, M.Nishio, S.Yokoyama, T.H.Tahirov. Crystal Structure of Ternary Complex of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase with Substrate Mimic and Co-Factoer To Be Published.