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Sodium in PDB 8owm: Crystal Structure of Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate

Enzymatic activity of Crystal Structure of Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate

All present enzymatic activity of Crystal Structure of Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate:
1.4.1.3;

Protein crystallography data

The structure of Crystal Structure of Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate, PDB code: 8owm 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) 65.70 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 95.544, 95.629, 95.841, 90.42, 93.59, 117.78
R / Rfree (%) 14.4 / 17.2

Other elements in 8owm:

The structure of Crystal Structure of Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate (pdb code 8owm). 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 Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate, PDB code: 8owm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8owm

Go back to Sodium Binding Sites List in 8owm
Sodium binding site 1 out of 3 in the Crystal Structure of Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate


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 Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na511

b:34.9
occ:1.00
 O D:HOH604 2.3 48.5 1.0
O D:ASP44 2.3 33.3 1.0
O A:ASP44 2.4 30.9 1.0
O2 D:GOL505 2.5 54.7 1.0
O2 A:GOL507 2.5 53.8 1.0
O D:HOH814 2.5 43.0 1.0
O3 A:GOL507 2.9 61.6 1.0
C D:ASP44 3.4 32.2 1.0
C A:ASP44 3.5 28.6 1.0
C2 A:GOL507 3.5 55.0 1.0
C3 A:GOL507 3.8 59.3 1.0
C2 D:GOL505 3.8 48.0 1.0
CA D:ASP44 4.0 29.4 1.0
CA A:ASP44 4.1 29.4 1.0
CB D:ASP44 4.4 29.1 1.0
CB A:ASP44 4.4 29.9 1.0
O D:HOH736 4.5 29.8 1.0
O A:HOH784 4.5 31.8 1.0
N D:ASP45 4.5 30.8 1.0
O1 D:GOL505 4.5 66.8 1.0
N A:ASP45 4.6 27.8 1.0
C3 D:GOL505 4.7 62.2 1.0
O A:HOH872 4.8 52.5 1.0
C1 D:GOL505 4.8 61.2 1.0
CA D:ASP45 4.8 31.9 1.0
CA A:ASP45 4.9 31.6 1.0
C1 A:GOL507 4.9 61.4 1.0

Sodium binding site 2 out of 3 in 8owm

Go back to Sodium Binding Sites List in 8owm
Sodium binding site 2 out of 3 in the Crystal Structure of Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate


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 Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na516

b:30.9
occ:1.00
 O B:HOH601 2.3 48.6 1.0
O2 B:GOL512 2.3 49.5 0.8
O B:ASP44 2.3 30.9 1.0
O F:ASP44 2.4 33.2 1.0
O3 B:GOL513 2.4 46.6 0.8
O B:HOH727 2.5 37.1 1.0
O2 B:GOL513 2.6 48.0 0.8
C3 B:GOL513 3.1 53.9 0.8
C2 B:GOL513 3.2 49.6 0.8
C B:ASP44 3.4 30.7 1.0
C F:ASP44 3.5 30.7 1.0
C2 B:GOL512 3.5 45.9 0.8
C3 B:GOL512 3.9 49.8 0.8
CA B:ASP44 4.0 26.8 1.0
CA F:ASP44 4.1 26.3 1.0
CB B:ASP44 4.4 27.0 1.0
O F:HOH749 4.5 28.4 1.0
CB F:ASP44 4.5 27.6 1.0
N B:ASP45 4.5 29.1 1.0
N F:ASP45 4.6 28.3 1.0
C1 B:GOL512 4.6 56.2 0.8
O B:HOH760 4.6 29.1 1.0
O B:HOH694 4.6 47.3 1.0
C1 B:GOL513 4.7 54.4 0.8
CA F:ASP45 4.8 27.8 1.0
CA B:ASP45 4.8 32.7 1.0

Sodium binding site 3 out of 3 in 8owm

Go back to Sodium Binding Sites List in 8owm
Sodium binding site 3 out of 3 in the Crystal Structure of Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate


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 Glutamate Dehydrogenase 2 From Arabidopsis Thaliana Binding Ca, Nad and 2,2-Dihydroxyglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na514

b:33.3
occ:1.00
 O C:ASP44 2.3 31.4 1.0
O E:ASP44 2.4 33.0 1.0
O C:HOH910 2.4 40.5 1.0
O1 C:GOL511 2.4 50.7 1.0
O1 E:GOL4201 2.7 60.9 1.0
C1 E:GOL4201 2.7 60.6 1.0
O2 C:GOL511 3.0 52.8 1.0
O2 E:GOL4201 3.2 55.4 1.0
C2 E:GOL4201 3.4 61.4 1.0
C C:ASP44 3.5 29.5 1.0
C E:ASP44 3.5 29.8 1.0
C1 C:GOL511 3.6 55.9 1.0
C2 C:GOL511 3.7 54.3 1.0
CA E:ASP44 4.0 28.0 1.0
CA C:ASP44 4.0 31.6 1.0
CB E:ASP44 4.4 27.1 1.0
O E:HOH4486 4.4 29.4 1.0
CB C:ASP44 4.4 34.7 1.0
O C:HOH794 4.4 28.1 1.0
N C:ASP45 4.6 30.5 1.0
N E:ASP45 4.6 33.2 1.0
C3 E:GOL4201 4.8 68.2 1.0
CA C:ASP45 4.8 34.0 1.0
CA E:ASP45 4.9 31.6 1.0

Reference:

M.Grzechowiak, J.Sliwiak, M.Jaskolski, M.Ruszkowski. Structural and Functional Studies of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 2 Demonstrate Enzyme Dynamics and Identify Its Calcium Binding Site. Plant Physiol Biochem. V. 201 07895 2023.
ISSN: ESSN 1873-2690
PubMed: 37478728
DOI: 10.1016/J.PLAPHY.2023.107895
Page generated: Mon Aug 18 14:56:16 2025

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