Sodium in PDB 2j40: 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound Inhibitor L-Proline and Nad.

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

The structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound Inhibitor L-Proline and Nad., PDB code: 2j40 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)	30.00 / 2.1
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	102.043, 102.043, 278.600, 90.00, 90.00, 120.00
R / Rfree (%)	14 / 18.9

The binding sites of Sodium atom in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound Inhibitor L-Proline and Nad. (pdb code 2j40). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound Inhibitor L-Proline and Nad., PDB code: 2j40:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound Inhibitor L-Proline 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 Thermophilus with Bound Inhibitor L-Proline and Nad. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1522 b:21.1 occ:1.00 O A:HOH2199 2.2 28.7 1.0 O A:LEU56 2.6 17.3 1.0 O A:HOH2293 2.6 26.6 1.0 OG A:SER55 2.8 18.5 1.0 O A:ASP211 2.9 17.4 1.0 O A:GLU123 3.0 15.1 1.0 N A:LEU56 3.4 17.7 1.0 CG A:GLU123 3.6 15.1 1.0 C A:LEU56 3.7 17.5 1.0 C A:ASP211 3.8 16.5 1.0 C A:SER55 3.9 17.8 1.0 CB A:SER55 4.0 17.2 1.0 C A:GLU123 4.0 13.6 1.0 CA A:SER55 4.1 17.5 1.0 CA A:LEU56 4.1 17.7 1.0 CA A:ASP211 4.1 17.1 1.0 O A:HOH2294 4.2 23.6 1.0 OE1 A:GLU123 4.3 13.4 1.0 CB A:ASP211 4.4 18.5 1.0 CD A:GLU123 4.4 14.6 1.0 CA A:GLU123 4.4 13.8 1.0 OD1 A:ASP211 4.5 23.9 1.0 CB A:GLU123 4.6 13.9 1.0 CD A:PRO58 4.8 15.3 1.0 O A:SER55 4.8 17.4 1.0 CB A:LEU56 4.8 18.0 1.0 N A:ASN57 4.9 15.8 1.0 N A:ALA212 4.9 14.6 1.0 CG A:ASP211 5.0 20.0 1.0

Sodium binding site 2 out of 3 in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound Inhibitor L-Proline 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 Thermophilus with Bound Inhibitor L-Proline and Nad. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1526 b:17.9 occ:0.50 NA B:NA1526 0.0 17.9 0.5 NA B:NA1526 1.5 14.4 0.5 O B:HOH2071 2.5 32.2 1.0 OG B:SER55 2.6 20.4 1.0 O B:ASP211 2.7 18.2 1.0 O B:HOH2259 2.9 35.9 1.0 O B:LEU56 3.1 19.4 1.0 N B:LEU56 3.4 20.6 1.0 C B:ASP211 3.5 17.4 1.0 O B:GLU123 3.5 18.7 1.0 CB B:SER55 3.7 20.2 1.0 CA B:ASP211 3.8 17.9 1.0 CG B:GLU123 3.8 17.0 1.0 CA B:SER55 3.8 20.9 1.0 C B:SER55 3.9 20.8 1.0 C B:LEU56 4.1 19.9 1.0 OE1 B:GLU123 4.2 16.1 1.0 OD1 B:ASP211 4.2 24.5 1.0 CB B:ASP211 4.2 18.1 1.0 CA B:LEU56 4.2 20.1 1.0 CD B:GLU123 4.5 18.2 1.0 C B:GLU123 4.5 17.4 1.0 N B:ALA212 4.6 16.9 1.0 O B:HOH2258 4.6 34.5 1.0 CG B:ASP211 4.7 20.0 1.0 O B:GLU210 4.8 17.3 1.0 CB B:LEU56 4.9 19.3 1.0 CA B:GLU123 4.9 17.0 1.0 O B:SER55 4.9 20.9 1.0 CB B:GLU123 5.0 16.8 1.0

Sodium binding site 3 out of 3 in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound Inhibitor L-Proline and Nad.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound Inhibitor L-Proline and Nad. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1526 b:14.4 occ:0.50 NA B:NA1526 0.0 14.4 0.5 NA B:NA1526 1.5 17.9 0.5 O B:HOH2259 2.2 35.9 1.0 O B:GLU123 2.2 18.7 1.0 O B:LEU56 2.5 19.4 1.0 O B:ASP211 3.1 18.2 1.0 O B:HOH2071 3.2 32.2 1.0 C B:GLU123 3.4 17.4 1.0 C B:LEU56 3.7 19.9 1.0 CG B:GLU123 3.7 17.0 1.0 OG B:SER55 3.8 20.4 1.0 CD B:PRO58 3.9 19.6 1.0 N B:LEU56 4.0 20.6 1.0 CA B:GLU123 4.1 17.0 1.0 C B:ASP211 4.2 17.4 1.0 O B:HOH2258 4.2 34.5 1.0 CA B:LEU56 4.4 20.1 1.0 N B:VAL124 4.4 16.9 1.0 O B:VAL364 4.4 20.8 1.0 OD1 B:ASP211 4.5 24.5 1.0 CB B:ASP211 4.5 18.1 1.0 CA B:ASP211 4.5 17.9 1.0 CB B:GLU123 4.6 16.8 1.0 CA B:VAL124 4.6 17.6 1.0 N B:PRO58 4.7 19.4 1.0 CG B:PRO58 4.7 18.7 1.0 CG1 B:VAL124 4.8 16.1 1.0 C B:SER55 4.8 20.8 1.0 N B:ASN57 4.8 19.2 1.0 CG2 B:VAL364 4.8 18.7 1.0 CD B:GLU123 4.9 18.2 1.0 OE1 B:GLU123 4.9 16.1 1.0 CB B:LEU56 4.9 19.3 1.0 CB B:SER55 5.0 20.2 1.0 CG B:ASP211 5.0 20.0 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.