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

Protein crystallography data

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

Other elements in 8s3d:

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:

Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8s3d

Go back to Calcium Binding Sites List in 8s3d
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca512

b:19.6
occ:1.00
 OE2 E:GLU38 2.2 19.9 1.0
O A:ILE30 2.3 18.4 1.0
O A:HOH645 2.3 24.1 1.0
O A:SER27 2.3 20.5 1.0
O A:HOH769 2.4 20.9 1.0
O E:HOH891 2.4 28.6 1.0
CD E:GLU38 3.4 18.9 1.0
C A:SER27 3.5 18.4 1.0
C A:ILE30 3.5 18.6 1.0
OE1 E:GLU38 4.0 20.3 1.0
OG A:SER27 4.0 18.9 1.0
CA A:LEU28 4.2 17.7 1.0
O A:LEU28 4.2 19.9 1.0
C A:LEU28 4.2 20.6 1.0
O A:HIS58 4.2 16.4 1.0
N A:LEU28 4.3 17.6 1.0
N A:TYR32 4.3 16.3 1.0
CA A:ILE30 4.3 17.9 1.0
N A:ILE30 4.3 19.3 1.0
C A:PRO31 4.3 15.5 1.0
OD2 A:ASP59 4.4 25.4 1.0
CB A:ILE30 4.4 17.8 1.0
CA A:SER27 4.4 18.3 1.0
N A:PRO31 4.5 19.5 1.0
CG E:GLU38 4.6 17.3 1.0
CA A:PRO31 4.6 17.0 1.0
O A:HOH894 4.6 22.8 1.0
CB E:GLU38 4.7 16.0 1.0
O A:HOH644 4.8 19.9 1.0
O A:PRO31 4.8 18.1 1.0
O E:HOH818 4.8 29.8 1.0
CB A:SER27 4.8 22.1 1.0
CA A:TYR32 4.9 15.4 1.0
N A:LEU29 4.9 18.8 1.0
C A:LEU29 4.9 23.2 1.0
C1 A:EDO507 5.0 37.4 1.0
CG2 A:ILE30 5.0 19.3 1.0

Calcium binding site 2 out of 6 in 8s3d

Go back to Calcium Binding Sites List in 8s3d
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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:Ca511

b:18.3
occ:1.00
 OE2 D:GLU38 2.3 18.6 1.0
O B:HOH712 2.3 22.2 1.0
O B:SER27 2.3 18.6 1.0
O B:HOH788 2.3 18.9 1.0
O B:ILE30 2.3 19.5 1.0
O D:HOH796 2.4 25.2 1.0
CD D:GLU38 3.4 20.1 1.0
C B:SER27 3.4 18.0 1.0
C B:ILE30 3.6 19.2 1.0
OG B:SER27 4.0 19.5 1.0
OE1 D:GLU38 4.0 19.1 1.0
CA B:LEU28 4.1 19.4 1.0
N B:LEU28 4.2 18.0 1.0
N B:ILE30 4.2 20.0 1.0
C B:LEU28 4.2 20.2 1.0
O B:LEU28 4.3 21.3 1.0
CA B:ILE30 4.3 19.5 1.0
O B:HIS58 4.3 16.5 1.0
N B:TYR32 4.3 16.0 1.0
C B:PRO31 4.4 15.9 1.0
OD2 B:ASP59 4.4 23.5 1.0
CA B:SER27 4.4 19.0 1.0
CB B:ILE30 4.4 17.7 1.0
N B:PRO31 4.6 18.1 1.0
O B:HOH892 4.6 20.8 1.0
CG D:GLU38 4.6 17.3 1.0
CA B:PRO31 4.6 15.4 1.0
CB D:GLU38 4.7 20.2 1.0
O B:HOH618 4.7 19.0 1.0
O D:HOH610 4.8 25.4 1.0
O B:PRO31 4.8 16.5 1.0
CB B:SER27 4.8 19.7 1.0
N B:LEU29 4.9 19.9 1.0
C B:LEU29 4.9 23.6 1.0
CA B:TYR32 4.9 16.6 1.0

Calcium binding site 3 out of 6 in 8s3d

Go back to Calcium Binding Sites List in 8s3d
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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
C:Ca511

b:19.0
occ:1.00
 OE2 F:GLU38 2.3 20.9 1.0
O C:SER27 2.3 17.4 1.0
O C:ILE30 2.3 17.7 1.0
O F:HOH2640 2.4 29.4 1.0
O C:HOH767 2.5 18.4 1.0
O C:HOH635 2.5 25.2 1.0
CD F:GLU38 3.4 21.2 1.0
C C:SER27 3.4 17.8 1.0
C C:ILE30 3.5 19.2 1.0
OE1 F:GLU38 3.9 19.2 1.0
OG C:SER27 4.0 20.4 1.0
CA C:LEU28 4.1 18.5 1.0
N C:LEU28 4.2 18.5 1.0
O C:LEU28 4.2 20.1 1.0
N C:ILE30 4.2 19.1 1.0
C C:LEU28 4.2 17.7 1.0
CA C:ILE30 4.2 17.2 1.0
O C:HIS58 4.3 15.3 1.0
N C:TYR32 4.3 16.1 1.0
CB C:ILE30 4.3 19.1 1.0
C C:PRO31 4.4 17.1 1.0
CA C:SER27 4.4 18.5 1.0
OD2 C:ASP59 4.4 26.9 1.0
N C:PRO31 4.5 18.3 1.0
CG F:GLU38 4.6 20.2 1.0
O C:HOH888 4.6 23.6 1.0
CA C:PRO31 4.6 17.0 1.0
CB F:GLU38 4.7 17.9 1.0
O C:HOH625 4.7 20.2 1.0
O2 F:EDO2302 4.7 45.4 1.0
O C:PRO31 4.8 18.6 1.0
O F:HOH2628 4.9 26.9 1.0
CB C:SER27 4.9 20.8 1.0
C C:LEU29 4.9 24.4 1.0
N C:LEU29 4.9 18.4 1.0
CG2 C:ILE30 4.9 21.1 1.0
CA C:TYR32 4.9 17.4 1.0

Calcium binding site 4 out of 6 in 8s3d

Go back to Calcium Binding Sites List in 8s3d
Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca binding site number 4 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:Ca509

b:19.2
occ:1.00
 OE2 B:GLU38 2.3 19.1 1.0
O D:SER27 2.3 18.9 1.0
O D:ILE30 2.3 19.4 1.0
O D:HOH719 2.4 24.9 1.0
O B:HOH889 2.4 28.5 1.0
O D:HOH722 2.4 19.9 1.0
C D:SER27 3.4 19.6 1.0
CD B:GLU38 3.4 21.8 1.0
C D:ILE30 3.5 18.0 1.0
OG D:SER27 4.0 20.1 1.0
OE1 B:GLU38 4.0 20.3 1.0
CA D:LEU28 4.1 22.0 1.0
N D:LEU28 4.2 21.3 1.0
N D:ILE30 4.2 18.8 1.0
C D:LEU28 4.3 21.1 1.0
CA D:ILE30 4.3 19.6 1.0
O D:HIS58 4.3 19.1 1.0
O D:LEU28 4.3 21.1 1.0
CA D:SER27 4.4 19.9 1.0
OD2 D:ASP59 4.4 27.3 1.0
N D:TYR32 4.4 16.8 1.0
C D:PRO31 4.4 18.3 1.0
CB D:ILE30 4.4 18.9 1.0
N D:PRO31 4.5 20.5 1.0
CG B:GLU38 4.5 18.2 1.0
O D:HOH609 4.6 21.4 1.0
CA D:PRO31 4.6 17.1 1.0
O D:HOH857 4.6 25.2 1.0
CB B:GLU38 4.7 17.4 1.0
O B:HOH602 4.8 28.6 1.0
CB D:SER27 4.8 20.1 1.0
O D:PRO31 4.8 18.3 1.0
C D:LEU29 4.9 22.8 1.0
N D:LEU29 4.9 21.3 1.0
CA D:TYR32 5.0 18.3 1.0

Calcium binding site 5 out of 6 in 8s3d

Go back to Calcium Binding Sites List in 8s3d
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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
E:Ca509

b:18.1
occ:1.00
 OE2 A:GLU38 2.2 18.7 1.0
O E:SER27 2.2 15.6 1.0
O E:ILE30 2.3 15.8 1.0
O E:HOH683 2.3 20.3 1.0
O A:HOH868 2.4 23.8 1.0
O E:HOH782 2.4 18.3 1.0
C E:SER27 3.4 15.4 1.0
CD A:GLU38 3.4 20.1 1.0
C E:ILE30 3.5 17.1 1.0
OE1 A:GLU38 4.0 15.8 1.0
OG E:SER27 4.0 18.2 1.0
CA E:LEU28 4.2 15.9 1.0
N E:LEU28 4.2 15.5 1.0
N E:ILE30 4.2 16.7 1.0
O E:HIS58 4.2 14.7 1.0
O E:LEU28 4.3 19.3 1.0
CA E:ILE30 4.3 15.3 1.0
C E:LEU28 4.3 17.2 1.0
N E:TYR32 4.3 14.7 1.0
OD2 E:ASP59 4.3 22.2 1.0
CA E:SER27 4.3 16.6 1.0
C E:PRO31 4.3 14.2 1.0
CB E:ILE30 4.4 15.1 1.0
N E:PRO31 4.5 14.6 1.0
CG A:GLU38 4.6 17.1 1.0
CA E:PRO31 4.6 17.0 1.0
O E:HOH868 4.6 19.8 1.0
CB A:GLU38 4.7 16.4 1.0
O E:HOH625 4.7 17.8 1.0
O A:HOH610 4.7 27.0 1.0
CB E:SER27 4.8 18.4 1.0
O E:PRO31 4.8 16.7 1.0
CA E:TYR32 4.9 16.0 1.0
C E:LEU29 4.9 18.7 1.0
N E:LEU29 4.9 17.4 1.0
CG2 E:ILE30 5.0 19.4 1.0

Calcium binding site 6 out of 6 in 8s3d

Go back to Calcium Binding Sites List in 8s3d
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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
F:Ca2312

b:18.0
occ:1.00
 O F:HOH2498 2.2 22.5 1.0
OE2 C:GLU38 2.3 19.4 1.0
O F:ILE30 2.3 14.2 1.0
O C:HOH821 2.3 23.8 1.0
O F:SER27 2.3 16.7 1.0
O F:HOH2512 2.4 17.6 1.0
C F:SER27 3.4 17.4 1.0
CD C:GLU38 3.5 19.8 1.0
C F:ILE30 3.5 15.1 1.0
OG F:SER27 4.0 16.6 1.0
OE1 C:GLU38 4.0 19.9 1.0
CA F:LEU28 4.1 16.7 1.0
O F:LEU28 4.2 17.9 1.0
N F:LEU28 4.2 17.0 1.0
N F:ILE30 4.2 16.8 1.0
C F:LEU28 4.2 15.3 1.0
CA F:ILE30 4.2 18.4 1.0
O F:HIS58 4.3 15.4 1.0
N F:TYR32 4.3 15.0 1.0
OD2 F:ASP59 4.3 23.5 1.0
CB F:ILE30 4.4 16.4 1.0
C F:PRO31 4.4 17.3 1.0
CA F:SER27 4.4 16.2 1.0
N F:PRO31 4.5 16.5 1.0
CA F:PRO31 4.6 17.2 1.0
O C:HOH736 4.6 24.2 1.0
O F:HOH2421 4.6 16.4 1.0
CG C:GLU38 4.6 17.1 1.0
O F:HOH2691 4.7 19.9 1.0
CB C:GLU38 4.7 17.0 1.0
O F:PRO31 4.8 17.1 1.0
CB F:SER27 4.8 16.5 1.0
C F:LEU29 4.9 21.1 1.0
N F:LEU29 4.9 17.9 1.0
CA F:TYR32 4.9 18.1 1.0
CG2 F:ILE30 5.0 18.3 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: Sat Sep 28 09:03:19 2024

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