Sodium in PDB 8s3d: Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) and Nad

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) and Nad, PDB code: 8s3d 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)	65.89 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.832, 155.707, 163.089, 90, 90, 90
R / Rfree (%)	14.7 / 17.4

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) and Nad also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) and Nad (pdb code 8s3d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) and Nad, PDB code: 8s3d:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) 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 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) and Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Na513 b:28.7 occ:1.00 O A:ASP44 2.3 22.6 1.0 O C:ASP44 2.3 21.7 1.0 O A:HOH943 2.4 28.8 1.0 O3 A:PG4511 2.5 52.2 1.0 O4 A:PG4511 2.9 55.0 1.0 O2 A:PG4511 2.9 50.9 1.0 C2 A:PG4511 3.2 34.6 1.0 C6 A:PG4511 3.3 56.8 1.0 C A:ASP44 3.4 21.4 1.0 C5 A:PG4511 3.4 56.5 1.0 C C:ASP44 3.5 20.2 1.0 C3 A:PG4511 3.5 54.5 1.0 C4 A:PG4511 3.6 55.1 1.0 O5 A:PG4511 3.6 42.8 1.0 CA A:ASP44 3.9 19.6 1.0 CA C:ASP44 4.0 16.9 1.0 C7 A:PG4511 4.1 51.6 1.0 CB A:ASP44 4.3 21.6 1.0 C8 A:PG4511 4.3 38.5 1.0 O A:HOH811 4.4 19.2 1.0 CB C:ASP44 4.4 20.9 1.0 O A:HOH809 4.4 45.5 1.0 O A:HOH702 4.5 38.9 1.0 O C:HOH672 4.5 18.1 1.0 N A:ASP45 4.5 19.0 1.0 N C:ASP45 4.6 19.9 1.0 C1 A:PG4511 4.7 38.5 1.0 CA A:ASP45 4.8 23.5 1.0 CA C:ASP45 4.8 23.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) 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 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) and Nad within 5.0Å range: probe atom residue distance (Å) B Occ B:Na512 b:34.0 occ:1.00 O B:ASP44 2.3 23.5 1.0 O F:ASP44 2.3 25.1 1.0 O B:HOH915 2.4 27.9 1.0 O F:HOH2489 2.4 40.5 1.0 O1 F:EDO2301 2.5 45.5 1.0 O1 B:EDO510 2.8 50.7 1.0 C1 B:EDO510 2.8 35.3 1.0 C1 F:EDO2301 3.3 38.7 1.0 C B:ASP44 3.4 21.9 1.0 C F:ASP44 3.4 21.0 1.0 CA B:ASP44 4.0 23.6 1.0 CA F:ASP44 4.1 22.2 1.0 O B:HOH951 4.3 46.2 1.0 C2 B:EDO510 4.3 39.4 1.0 CB B:ASP44 4.4 22.4 1.0 CB F:ASP44 4.5 20.7 1.0 O B:HOH739 4.5 22.0 1.0 O F:HOH2564 4.5 20.5 1.0 N B:ASP45 4.5 20.3 1.0 N F:ASP45 4.5 21.8 1.0 C2 F:EDO2301 4.6 43.6 1.0 CA B:ASP45 4.7 27.1 1.0 CA F:ASP45 4.8 24.6 1.0 O2 B:EDO510 5.0 52.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with 2-Amino-2-Hydroxyglutarate (Reaction Intermediate) and Nad within 5.0Å range: probe atom residue distance (Å) B Occ D:Na510 b:35.2 occ:1.00 O3 E:PG4507 2.2 46.2 1.0 O E:ASP44 2.2 23.0 1.0 O D:ASP44 2.3 22.9 1.0 O D:HOH873 2.3 27.2 1.0 O2 E:PG4507 2.3 47.4 1.0 O4 E:PG4507 2.9 58.9 1.0 C4 E:PG4507 2.9 42.5 1.0 C3 E:PG4507 3.0 44.9 1.0 C2 E:PG4507 3.2 34.5 1.0 C5 E:PG4507 3.2 54.1 1.0 C7 E:PG4507 3.3 35.5 1.0 C6 E:PG4507 3.3 45.4 1.0 C E:ASP44 3.3 23.4 1.0 C D:ASP44 3.4 21.9 1.0 CA E:ASP44 3.9 21.9 1.0 CA D:ASP44 4.0 21.4 1.0 CB E:ASP44 4.2 20.3 1.0 O D:HOH749 4.4 20.4 1.0 CB D:ASP44 4.4 20.0 1.0 O E:HOH784 4.4 20.7 1.0 N E:ASP45 4.4 22.3 1.0 N D:ASP45 4.5 20.7 1.0 C1 E:PG4507 4.6 41.6 1.0 CA D:ASP45 4.7 21.3 1.0 C8 E:PG4507 4.7 47.3 1.0 CA E:ASP45 4.7 27.6 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