Sodium in PDB 2bhp: Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad.

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

The structure of Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad., PDB code: 2bhp was solved by E.Inagaki, T.H.Tahirov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.76 / 1.8
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	102.179, 102.179, 278.614, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 17.6

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

Sodium binding site 1 out of 2 in the Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad.


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. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1526 b:19.4 occ:1.00 O A:HOH2449 2.4 25.7 1.0 O A:LEU56 2.6 10.9 1.0 O A:HOH2150 2.7 31.1 1.0 O A:GLU123 2.8 4.5 1.0 O A:ASP211 2.8 10.1 1.0 OG A:SER55 2.9 11.6 1.0 CG A:GLU123 3.5 6.8 1.0 N A:LEU56 3.6 10.2 1.0 C A:LEU56 3.7 11.6 1.0 C A:ASP211 3.8 10.0 1.0 C A:GLU123 3.8 7.4 1.0 C A:SER55 4.0 9.9 1.0 CB A:SER55 4.1 9.6 1.0 CA A:ASP211 4.1 10.4 1.0 CA A:SER55 4.2 8.8 1.0 CA A:LEU56 4.2 10.1 1.0 CA A:GLU123 4.3 5.7 1.0 O A:HOH2450 4.3 20.1 1.0 CB A:ASP211 4.3 10.7 1.0 OE1 A:GLU123 4.4 5.3 1.0 CD A:GLU123 4.5 8.6 1.0 CB A:GLU123 4.5 6.0 1.0 CD A:PRO58 4.5 7.2 1.0 OD1 A:ASP211 4.6 20.6 1.0 O A:SER55 4.9 12.4 1.0 N A:ASN57 4.9 8.2 1.0 N A:ALA212 4.9 8.3 1.0 N A:VAL124 5.0 5.3 1.0 CB A:LEU56 5.0 8.8 1.0

Sodium binding site 2 out of 2 in the Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nad.


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. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1524 b:22.6 occ:1.00 O B:HOH2436 2.5 25.4 1.0 O B:LEU56 2.5 9.9 1.0 O B:GLU123 2.6 6.7 1.0 O B:HOH2143 2.9 37.8 1.0 O B:ASP211 3.0 13.2 1.0 OG B:SER55 3.1 16.3 1.0 CG B:GLU123 3.4 8.9 1.0 N B:LEU56 3.6 10.1 1.0 C B:LEU56 3.6 10.9 1.0 C B:GLU123 3.7 7.3 1.0 C B:ASP211 4.0 12.8 1.0 CA B:LEU56 4.1 11.5 1.0 CA B:GLU123 4.1 6.7 1.0 C B:SER55 4.2 12.3 1.0 CB B:SER55 4.3 13.4 1.0 CA B:ASP211 4.4 11.1 1.0 O B:HOH2435 4.4 22.7 1.0 CA B:SER55 4.4 11.8 1.0 CD B:PRO58 4.4 10.0 1.0 CB B:GLU123 4.4 7.7 1.0 OE1 B:GLU123 4.5 8.2 1.0 CD B:GLU123 4.5 11.2 1.0 CB B:ASP211 4.6 12.6 1.0 OD1 B:ASP211 4.7 21.3 1.0 N B:ASN57 4.8 9.6 1.0 N B:VAL124 4.8 8.1 1.0 CB B:LEU56 4.9 10.3 1.0 CG2 B:VAL65 4.9 19.9 1.0

E.Inagaki, N.Ohshima, H.Takahashi, C.Kuroishi, S.Yokoyama, T.H.Tahirov. Crystal Structure of Thermus Thermophilus Delta(1)- Pyrroline-5-Carboxylate Dehydrogenase. J.Mol.Biol. V. 362 490 2006.
ISSN: ISSN 0022-2836
PubMed: 16934832
DOI: 10.1016/J.JMB.2006.07.048