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

Protein crystallography data

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

Other elements in 8s39:

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

Sodium Binding Sites:

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 8s39

Go back to Sodium Binding Sites List in 8s39
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 8s39

Go back to Sodium Binding Sites List in 8s39
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

Reference:

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
Page generated: Wed Oct 9 13:25:15 2024

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