Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 in Complex with Citrate and Nad, PDB code: 8s38:
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 Citrate 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 Citrate and Nad within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca515 b:35.4 occ:1.00 OE1 A:GLU38 2.3 31.8 1.0 O A:HOH755 2.3 39.0 1.0 CD A:GLU38 3.4 39.0 1.0 OE2 A:GLU38 3.9 41.8 1.0 CG A:GLU38 4.6 30.1 1.0 CB A:GLU38 4.8 29.0 1.0 O A:HOH717 5.0 36.6 1.0

Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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:Ca514 b:35.6 occ:1.00 O B:HOH720 2.3 33.1 1.0 O B:SER27 2.3 30.8 1.0 O B:ILE30 2.3 30.3 1.0 O B:HOH722 2.5 33.9 1.0 C B:SER27 3.4 32.2 1.0 C B:ILE30 3.5 32.8 1.0 OG B:SER27 4.0 34.2 1.0 CA B:LEU28 4.1 32.4 1.0 C B:LEU28 4.2 30.4 1.0 N B:LEU28 4.2 30.1 1.0 N B:ILE30 4.2 30.9 1.0 O B:LEU28 4.2 34.3 1.0 CA B:ILE30 4.3 28.4 1.0 O B:HIS58 4.3 26.2 1.0 N B:TYR32 4.3 29.1 1.0 CA B:SER27 4.4 30.6 1.0 C B:PRO31 4.4 28.6 1.0 CB B:ILE30 4.4 33.0 1.0 OD2 B:ASP59 4.4 33.8 1.0 N B:PRO31 4.5 30.2 1.0 CA B:PRO31 4.6 28.0 1.0 O B:HOH616 4.6 27.9 1.0 O B:HOH768 4.8 30.7 1.0 N B:LEU29 4.8 34.9 1.0 CB B:SER27 4.8 30.9 1.0 O B:PRO31 4.8 28.7 1.0 CA B:TYR32 4.9 30.6 1.0 C B:LEU29 4.9 38.2 1.0

Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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 C:Ca1415 b:45.5 occ:1.00 O C:HOH1639 2.1 31.1 1.0 O C:SER27 2.3 35.2 1.0 O C:ILE30 2.4 30.5 1.0 O C:HOH1682 2.8 43.5 1.0 C C:SER27 3.5 38.5 1.0 C C:ILE30 3.6 33.8 1.0 O C:LEU28 4.0 36.5 1.0 CA C:LEU28 4.1 29.8 1.0 O C:HIS58 4.1 29.1 1.0 C C:LEU28 4.1 33.9 1.0 N C:LEU28 4.3 30.7 1.0 N C:TYR32 4.3 29.3 1.0 OD2 C:ASP59 4.3 35.8 1.0 N C:ILE30 4.3 32.2 1.0 OG C:SER27 4.4 48.1 1.0 CA C:ILE30 4.4 31.9 1.0 C C:PRO31 4.4 27.8 1.0 N C:PRO31 4.6 31.0 1.0 CA C:SER27 4.6 35.7 1.0 CB C:ILE30 4.6 32.3 1.0 CA C:PRO31 4.6 28.4 1.0 O C:HOH1700 4.7 31.7 1.0 N C:LEU29 4.7 33.1 1.0 C C:LEU29 4.8 35.0 1.0 O C:HOH1518 4.8 33.5 1.0 CA C:TYR32 4.9 27.4 1.0 O C:PRO31 4.9 29.7 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