Sodium in PDB 8s38: Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Citrate and Nad

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Citrate and Nad, PDB code: 8s38 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)	59.64 / 1.89
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.368, 163.1, 219.023, 90, 90, 90
R / Rfree (%)	15.8 / 18.7

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Citrate 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 Citrate and Nad (pdb code 8s38). 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 Citrate and Nad, PDB code: 8s38:
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 Citrate 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 Citrate and Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Na510 b:44.1 occ:1.00 O A:ASP44 2.3 38.1 1.0 O A:HOH814 2.3 45.5 1.0 O1 A:EDO514 2.4 57.9 1.0 O A:HOH605 2.5 53.2 1.0 O A:HOH821 2.9 57.8 1.0 C A:ASP44 3.4 37.7 1.0 C1 A:EDO514 3.5 55.9 1.0 CA A:ASP44 4.0 37.6 1.0 O2 A:PEG509 4.3 67.5 1.0 CB A:ASP44 4.4 37.9 1.0 O A:HOH721 4.5 36.9 1.0 N A:ASP45 4.5 37.8 1.0 C1 A:PEG509 4.5 49.7 1.0 C3 A:PEG509 4.6 61.4 1.0 C2 A:EDO514 4.7 52.9 1.0 CA A:ASP45 4.8 35.5 1.0 C2 A:PEG509 4.8 59.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Citrate 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 Citrate and Nad within 5.0Å range: probe atom residue distance (Å) B Occ B:Na509 b:49.4 occ:0.50 O B:HOH808 2.3 44.8 0.5 O B:ASP44 2.3 41.0 1.0 O B:HOH793 2.4 51.8 0.5 C B:ASP44 3.4 38.6 1.0 O B:HOH821 3.5 55.6 1.0 CA B:ASP44 4.0 38.7 1.0 CB B:ASP44 4.3 39.0 1.0 O B:HOH729 4.5 36.1 1.0 N B:ASP45 4.6 39.6 1.0 CA B:ASP45 4.9 38.4 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