Sodium in PDB 8s39: Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Isophthalic Acid and Nad

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Isophthalic Acid and Nad, PDB code: 8s39 was solved by M.Grzechowiak, M.Ruszkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.38 / 2.00
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.728, 162.769, 216.988, 90, 90, 90
R / Rfree (%)	16.3 / 21.2

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Isophthalic Acid and Nad also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Isophthalic Acid and Nad (pdb code 8s39). 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 Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Isophthalic Acid and Nad, PDB code: 8s39:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Isophthalic Acid and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Isophthalic Acid and Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1605 b:64.3 occ:1.00 O A:ASP44 2.2 50.9 1.0 C A:ASP44 3.3 40.0 1.0 O A:HOH1835 3.5 54.7 1.0 CA A:ASP44 3.8 40.7 1.0 CB A:ASP44 4.2 42.9 1.0 N A:ASP45 4.4 45.5 1.0 O A:HOH1756 4.5 38.9 1.0 CA A:ASP45 4.7 48.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Isophthalic Acid and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Isophthalic Acid and Nad within 5.0Å range: probe atom residue distance (Å) B Occ B:Na807 b:73.3 occ:0.50 O B:ASP44 2.4 47.8 1.0 C B:ASP44 3.4 40.2 1.0 O B:HOH1047 3.5 51.2 1.0 CA B:ASP44 3.9 41.0 1.0 O B:HOH1007 4.3 44.2 1.0 CB B:ASP44 4.3 51.9 1.0 N B:ASP45 4.6 48.9 1.0 CA B:ASP45 4.9 61.2 1.0

M.Grzechowiak, J.Sliwiak, A.Link, M.Ruszkowski. Legume-Type Glutamate Dehydrogenase: Structure, Activity, and Inhibition Studies. Int.J.Biol.Macromol. V. 278 34648 2024.
ISSN: ISSN 0141-8130
PubMed: 39142482
DOI: 10.1016/J.IJBIOMAC.2024.134648