Sodium in PDB 2ehq: Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nadp

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

The structure of Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nadp, PDB code: 2ehq 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)	22.11 / 1.55
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	102.426, 102.426, 278.837, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 18

The binding sites of Sodium atom in the Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus with Bound Nadp (pdb code 2ehq). 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 Nadp, PDB code: 2ehq:
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 Nadp


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 Nadp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1540 b:16.2 occ:1.00 O A:HOH1851 2.4 28.0 1.0 O A:HOH1716 2.4 18.9 1.0 O A:LEU56 2.6 11.2 1.0 O A:GLU123 2.7 7.6 1.0 O A:ASP211 2.7 12.0 1.0 OG A:SER55 2.8 12.0 1.0 CG A:GLU123 3.4 7.8 1.0 N A:LEU56 3.6 10.3 1.0 C A:LEU56 3.7 10.5 1.0 C A:ASP211 3.7 11.6 1.0 C A:GLU123 3.8 7.7 1.0 CB A:SER55 4.0 11.6 1.0 CA A:ASP211 4.1 11.9 1.0 C A:SER55 4.1 11.0 1.0 CA A:SER55 4.2 11.4 1.0 CA A:LEU56 4.2 10.4 1.0 CA A:GLU123 4.2 7.3 1.0 OE2 A:GLU123 4.3 8.8 1.0 CB A:ASP211 4.3 12.5 1.0 O A:HOH1735 4.3 18.6 1.0 CD A:GLU123 4.4 10.3 1.0 CB A:GLU123 4.5 7.8 1.0 CD A:PRO58 4.5 8.8 1.0 OD1 A:ASP211 4.6 17.6 1.0 N A:ASN57 4.8 10.4 1.0 N A:ALA212 4.8 10.8 1.0 N A:VAL124 4.9 7.4 1.0 O A:SER55 4.9 11.1 1.0 CB A:LEU56 4.9 10.0 1.0 CG A:ASP211 4.9 14.4 1.0

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


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 Nadp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2540 b:15.4 occ:1.00 O B:HOH3019 2.1 28.6 1.0 O B:HOH2790 2.4 23.1 1.0 O B:GLU123 2.5 8.4 1.0 O B:LEU56 2.5 11.1 1.0 O B:ASP211 2.9 11.7 1.0 OG B:SER55 3.2 12.7 1.0 CG B:GLU123 3.5 8.4 1.0 C B:GLU123 3.6 8.2 1.0 C B:LEU56 3.6 11.4 1.0 N B:LEU56 3.7 12.1 1.0 C B:ASP211 3.9 11.2 1.0 O B:HOH2818 4.1 29.0 1.0 CA B:GLU123 4.1 8.3 1.0 CA B:LEU56 4.2 11.5 1.0 CA B:ASP211 4.2 11.5 1.0 CD B:PRO58 4.3 9.8 1.0 C B:SER55 4.4 12.8 1.0 CB B:ASP211 4.4 12.4 1.0 CB B:SER55 4.4 13.4 1.0 CB B:GLU123 4.5 8.3 1.0 CD B:GLU123 4.6 9.3 1.0 CA B:SER55 4.6 12.8 1.0 OD1 B:ASP211 4.6 19.0 1.0 OE2 B:GLU123 4.6 10.4 1.0 N B:VAL124 4.7 8.2 1.0 N B:ASN57 4.8 9.9 1.0 CB B:LEU56 4.9 11.9 1.0 O B:VAL364 4.9 8.2 1.0 CG1 B:VAL124 4.9 8.6 1.0 CG2 B:VAL65 5.0 13.1 1.0 CA B:VAL124 5.0 8.0 1.0

E.Inagaki, N.Ohshima, K.Sakamoto, N.D.Babayeva, H.Kato, S.Yokoyama, T.H.Tahirov. New Insights Into the Binding Mode of Coenzymes: Structure of Thermus Thermophilus DELTA1-Pyrroline-5-Carboxylate Dehydrogenase Complexed with Nadp+. Acta Crystallogr.,Sect.F V. 63 462 2007.
ISSN: ESSN 1744-3091
PubMed: 17554163
DOI: 10.1107/S1744309107021422