Sodium in PDB 2iy6: 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Citrate

All present enzymatic activity of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Citrate:
1.5.1.12;

The structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Citrate, PDB code: 2iy6 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 / 1.80
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	102.047, 102.047, 278.901, 90.00, 90.00, 120.00
R / Rfree (%)	13.9 / 17

The structure of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Citrate also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Citrate (pdb code 2iy6). 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 with Bound Citrate, PDB code: 2iy6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Citrate


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 with Bound Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1540 b:19.3 occ:1.00 O A:HOH2130 2.3 32.6 1.0 O A:HOH2219 2.3 16.6 1.0 O A:LEU56 2.6 8.8 1.0 O A:ASP211 2.7 8.2 1.0 O A:GLU123 2.8 4.8 1.0 OG A:SER55 3.0 11.0 1.0 CG A:GLU123 3.5 5.4 1.0 N A:LEU56 3.6 9.6 1.0 C A:ASP211 3.7 7.8 1.0 C A:LEU56 3.7 9.0 1.0 C A:GLU123 3.8 5.1 1.0 CA A:ASP211 4.0 8.7 1.0 C A:SER55 4.1 9.9 1.0 CB A:SER55 4.2 10.1 1.0 CA A:LEU56 4.2 9.5 1.0 O A:HOH2424 4.2 24.5 1.0 CA A:SER55 4.3 9.9 1.0 CA A:GLU123 4.3 4.5 1.0 CB A:ASP211 4.3 8.7 1.0 OE1 A:GLU123 4.4 4.7 1.0 O A:HOH2129 4.4 25.9 1.0 CD A:GLU123 4.4 6.2 1.0 CB A:GLU123 4.5 4.3 1.0 CD A:PRO58 4.6 6.1 1.0 OD1 A:ASP211 4.6 15.4 1.0 N A:ALA212 4.8 7.5 1.0 N A:ASN57 4.8 7.5 1.0 O A:SER55 4.9 10.3 1.0 CB A:LEU56 5.0 9.9 1.0 N A:VAL124 5.0 4.4 1.0 CG A:ASP211 5.0 12.1 1.0

Sodium binding site 2 out of 2 in the 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Citrate


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 with Bound Citrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1540 b:17.7 occ:1.00 O B:HOH2116 2.1 23.4 1.0 O B:HOH2409 2.3 24.8 1.0 O B:GLU123 2.5 7.1 1.0 O B:LEU56 2.5 10.4 1.0 O B:ASP211 2.8 9.5 1.0 OG B:SER55 3.3 13.0 1.0 CG B:GLU123 3.5 6.2 1.0 C B:GLU123 3.6 7.0 1.0 C B:LEU56 3.7 10.8 1.0 N B:LEU56 3.7 11.6 1.0 C B:ASP211 3.8 8.8 1.0 CA B:GLU123 4.1 6.7 1.0 O B:HOH2408 4.2 27.7 1.0 CA B:ASP211 4.2 9.2 1.0 CD B:PRO58 4.2 7.6 1.0 CA B:LEU56 4.2 11.4 1.0 CB B:ASP211 4.4 9.7 1.0 CB B:GLU123 4.4 6.4 1.0 C B:SER55 4.4 12.1 1.0 CB B:SER55 4.5 12.8 1.0 CD B:GLU123 4.5 6.8 1.0 OE1 B:GLU123 4.6 5.7 1.0 CA B:SER55 4.6 12.3 1.0 N B:VAL124 4.7 6.7 1.0 OD1 B:ASP211 4.7 16.6 1.0 N B:ASN57 4.8 9.2 1.0 O B:VAL364 4.9 7.5 1.0 CB B:LEU56 4.9 12.0 1.0 CG2 B:VAL65 4.9 12.7 1.0 CG1 B:VAL124 4.9 7.0 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