Sodium in PDB 8s3c: Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded)

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded), PDB code: 8s3c 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)	47.83 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	95.651, 164.554, 195.412, 90, 90, 90
R / Rfree (%)	17.4 / 20.4

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded) 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 (Unliganded) (pdb code 8s3c). 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 (Unliganded), PDB code: 8s3c:
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 (Unliganded)


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 (Unliganded) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na506 b:70.7 occ:0.50 O B:ASP44 2.2 65.9 1.0 O B:HOH697 2.9 70.8 1.0 C B:ASP44 3.3 65.2 1.0 CA B:ASP44 4.0 62.2 1.0 CB B:ASP44 4.4 62.1 1.0 N B:ASP45 4.4 59.6 1.0 CA B:ASP45 4.6 64.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded)


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 (Unliganded) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na504 b:83.1 occ:1.00 O C:HOH664 2.6 72.6 1.0 O C:ASP44 3.0 70.7 1.0 C C:ASP44 4.1 71.8 1.0 CA C:ASP45 4.7 71.5 1.0 N C:ASP45 4.8 68.8 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