Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Isophthalic Acid and Nad, PDB code: 8s39:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca1606 b:45.3 occ:1.00 O A:HOH1762 2.3 47.3 1.0 O A:ILE30 2.4 39.1 1.0 O A:SER27 2.4 44.6 1.0 O A:HOH1770 2.5 38.4 1.0 C A:SER27 3.5 41.1 1.0 C A:ILE30 3.6 38.2 1.0 OG A:SER27 3.9 48.9 1.0 CA A:LEU28 4.1 46.2 1.0 N A:ILE30 4.2 44.5 1.0 N A:LEU28 4.2 40.7 1.0 C A:LEU28 4.3 49.4 1.0 CA A:ILE30 4.3 41.2 1.0 O A:HIS58 4.3 39.2 1.0 N A:TYR32 4.3 35.9 1.0 O A:LEU28 4.4 43.1 1.0 CB A:ILE30 4.4 43.3 1.0 C A:PRO31 4.4 39.4 1.0 CA A:SER27 4.5 41.8 1.0 OD2 A:ASP59 4.5 45.3 1.0 N A:PRO31 4.6 38.7 1.0 O A:HOH1715 4.6 38.2 1.0 CA A:PRO31 4.7 32.7 1.0 O A:HOH1811 4.7 42.0 1.0 O A:PRO31 4.8 38.3 1.0 CB A:SER27 4.8 42.8 1.0 N A:LEU29 4.9 35.7 1.0 CA A:TYR32 4.9 34.5 1.0

Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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:Ca808 b:47.1 occ:1.00 O B:ILE30 2.4 34.0 1.0 O B:HOH980 2.4 43.2 1.0 O B:SER27 2.4 40.6 1.0 O B:HOH961 2.5 35.9 1.0 C B:SER27 3.4 40.7 1.0 C B:ILE30 3.6 45.5 1.0 OG B:SER27 3.8 48.1 1.0 CA B:LEU28 4.1 44.7 1.0 O B:LEU28 4.1 44.6 1.0 C B:LEU28 4.1 38.8 1.0 N B:ILE30 4.2 46.2 1.0 N B:LEU28 4.2 41.6 1.0 CA B:ILE30 4.3 49.0 1.0 N B:TYR32 4.3 40.1 1.0 CB B:ILE30 4.4 48.4 1.0 CA B:SER27 4.4 41.7 1.0 OD1 B:ASP59 4.4 60.1 1.0 O B:HIS58 4.4 33.9 1.0 C B:PRO31 4.4 39.2 1.0 O B:HOH915 4.5 37.6 1.0 N B:PRO31 4.6 40.4 1.0 CA B:PRO31 4.6 33.5 1.0 CB B:SER27 4.7 43.5 1.0 N B:LEU29 4.8 39.5 1.0 O B:HOH1021 4.9 45.6 1.0 O B:PRO31 4.9 35.8 1.0 CG2 B:ILE30 4.9 45.9 1.0 CA B:TYR32 5.0 44.2 1.0 C B:LEU29 5.0 47.1 1.0

Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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:Ca809 b:60.6 occ:1.00 OE1 B:GLU38 2.3 54.9 1.0 O B:HOH925 2.7 111.6 1.0 CD B:GLU38 3.3 61.9 1.0 OE2 B:GLU38 3.8 62.9 1.0 CG B:GLU38 4.6 52.5 1.0 CB B:GLU38 4.8 46.6 1.0 O B:HOH1016 4.9 49.5 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