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Potassium in PDB 6yeh: Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form

Enzymatic activity of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form

All present enzymatic activity of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form:
1.4.1.3;

Protein crystallography data

The structure of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form, PDB code: 6yeh was solved by M.Ruszkowski, M.Grzechowiak, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.77 / 2.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.570, 99.169, 318.084, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.5

Potassium Binding Sites:

The binding sites of Potassium atom in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form (pdb code 6yeh). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form, PDB code: 6yeh:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 6yeh

Go back to Potassium Binding Sites List in 6yeh
Potassium binding site 1 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K505

b:44.6
occ:1.00
 OE2 B:GLU38 2.5 34.1 1.0
O A:SER27 2.6 38.1 1.0
O A:ILE30 2.6 24.9 1.0
CD B:GLU38 3.6 33.7 1.0
C A:SER27 3.6 34.0 1.0
C A:ILE30 3.9 25.6 1.0
OD2 A:ASP59 3.9 46.7 1.0
OE1 B:GLU38 3.9 32.9 1.0
CA A:LEU28 4.1 28.5 1.0
O A:HIS58 4.2 36.0 1.0
OG A:SER27 4.2 27.0 1.0
O A:LEU28 4.2 28.0 1.0
N A:LEU28 4.3 32.4 1.0
C A:LEU28 4.3 28.3 1.0
N A:PHE32 4.5 28.5 1.0
C A:PRO31 4.6 23.2 1.0
N A:ILE30 4.7 25.6 1.0
CA A:SER27 4.7 28.3 1.0
CA A:PRO31 4.7 23.4 1.0
CA A:ILE30 4.7 25.4 1.0
CG A:ASP59 4.8 41.0 1.0
N A:PRO31 4.8 24.4 1.0
CG B:GLU38 4.9 28.7 1.0
CB A:ILE30 5.0 25.9 1.0

Potassium binding site 2 out of 6 in 6yeh

Go back to Potassium Binding Sites List in 6yeh
Potassium binding site 2 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K506

b:47.6
occ:1.00
 O B:SER27 2.5 37.5 1.0
O B:ILE30 2.5 32.3 1.0
OE2 A:GLU38 2.6 50.6 1.0
CD A:GLU38 3.4 49.4 1.0
C B:SER27 3.5 36.0 1.0
OE1 A:GLU38 3.5 53.0 1.0
OD2 B:ASP59 3.6 49.6 1.0
C B:ILE30 3.7 33.5 1.0
CA B:LEU28 4.0 35.5 1.0
OG B:SER27 4.1 35.0 1.0
O B:LEU28 4.2 42.1 1.0
N B:LEU28 4.2 36.5 1.0
O B:HIS58 4.2 36.7 1.0
C B:LEU28 4.2 38.3 1.0
N B:ILE30 4.5 42.9 1.0
CA B:ILE30 4.5 35.7 1.0
CA B:SER27 4.6 37.5 1.0
N B:PHE32 4.6 42.6 1.0
C B:PRO31 4.7 39.5 1.0
CG B:ASP59 4.7 47.2 1.0
N B:PRO31 4.7 33.2 1.0
CB B:ILE30 4.7 35.9 1.0
CA B:PRO31 4.8 31.5 1.0
CG A:GLU38 4.8 41.1 1.0
CB B:SER27 4.9 37.2 1.0

Potassium binding site 3 out of 6 in 6yeh

Go back to Potassium Binding Sites List in 6yeh
Potassium binding site 3 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K501

b:39.2
occ:1.00
 O C:ILE30 2.5 38.8 1.0
O C:SER27 2.6 35.6 1.0
OE2 D:GLU38 2.6 41.6 1.0
O C:HOH610 3.4 35.7 1.0
CD D:GLU38 3.7 41.4 1.0
C C:SER27 3.7 38.6 1.0
C C:ILE30 3.7 37.0 1.0
O C:HIS58 4.0 38.9 1.0
OE1 D:GLU38 4.0 44.8 1.0
OD2 C:ASP59 4.0 53.1 1.0
CA C:LEU28 4.1 37.1 1.0
O C:LEU28 4.1 41.6 1.0
OG C:SER27 4.2 42.4 1.0
C C:LEU28 4.2 37.9 1.0
N C:LEU28 4.3 40.2 1.0
N C:PHE32 4.4 31.7 1.0
C C:PRO31 4.4 31.9 1.0
N C:ILE30 4.5 37.7 1.0
CA C:ILE30 4.6 37.5 1.0
CA C:PRO31 4.6 32.9 1.0
N C:PRO31 4.6 31.1 1.0
CA C:SER27 4.7 38.2 1.0
CB C:ILE30 4.8 35.0 1.0
O C:PRO31 4.8 37.1 1.0
CA C:PHE32 4.8 30.3 1.0
CG C:ASP59 4.9 47.7 1.0
CG D:GLU38 5.0 30.6 1.0
N C:LEU29 5.0 36.9 1.0

Potassium binding site 4 out of 6 in 6yeh

Go back to Potassium Binding Sites List in 6yeh
Potassium binding site 4 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K501

b:30.0
occ:1.00
 O D:SER27 2.6 32.6 1.0
OE2 C:GLU38 2.6 42.6 1.0
O D:ILE30 2.6 26.0 1.0
CD C:GLU38 3.5 38.8 1.0
C D:SER27 3.6 29.9 1.0
OE1 C:GLU38 3.7 44.6 1.0
OD2 D:ASP59 3.8 43.0 1.0
C D:ILE30 3.8 26.8 1.0
O D:HOH606 3.9 19.7 1.0
CA D:LEU28 4.0 31.6 1.0
OG D:SER27 4.0 40.0 1.0
O D:HIS58 4.1 30.2 1.0
O D:LEU28 4.1 40.4 1.0
C D:LEU28 4.2 32.2 1.0
N D:LEU28 4.2 31.6 1.0
N D:ILE30 4.6 29.6 1.0
N D:PHE32 4.6 25.2 1.0
CA D:ILE30 4.7 28.6 1.0
CA D:SER27 4.7 30.1 1.0
C D:PRO31 4.7 26.7 1.0
CG D:ASP59 4.7 41.7 1.0
N D:PRO31 4.8 26.3 1.0
CA D:PRO31 4.8 27.7 1.0
O C:HOH619 4.8 35.5 1.0
CB D:ILE30 4.9 28.9 1.0
CG C:GLU38 5.0 28.9 1.0
N D:LEU29 5.0 34.4 1.0
CB D:SER27 5.0 30.5 1.0

Potassium binding site 5 out of 6 in 6yeh

Go back to Potassium Binding Sites List in 6yeh
Potassium binding site 5 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K502

b:40.9
occ:1.00
 O E:SER27 2.6 50.9 1.0
O E:ILE30 2.6 43.2 1.0
OE2 F:GLU38 2.7 43.6 1.0
CD F:GLU38 3.5 44.0 1.0
OE1 F:GLU38 3.6 49.9 1.0
C E:SER27 3.7 45.3 1.0
C E:ILE30 3.8 41.5 1.0
O E:HOH601 3.9 30.3 1.0
OD2 E:ASP59 3.9 54.1 1.0
CA E:LEU28 4.1 41.1 1.0
OG E:SER27 4.1 46.3 1.0
O E:HIS58 4.1 48.5 1.0
O E:LEU28 4.1 41.4 1.0
C E:LEU28 4.2 41.4 1.0
N E:LEU28 4.3 44.1 1.0
N E:PHE32 4.5 42.1 1.0
C E:PRO31 4.6 43.3 1.0
N E:ILE30 4.6 43.7 1.0
CA E:ILE30 4.7 42.4 1.0
CA E:SER27 4.7 44.3 1.0
CA E:PRO31 4.7 40.2 1.0
N E:PRO31 4.8 39.1 1.0
CG E:ASP59 4.8 52.2 1.0
CB E:ILE30 4.9 43.3 1.0
CA E:PHE32 4.9 39.2 1.0
CG F:GLU38 5.0 38.7 1.0

Potassium binding site 6 out of 6 in 6yeh

Go back to Potassium Binding Sites List in 6yeh
Potassium binding site 6 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K505

b:39.2
occ:1.00
 OE2 E:GLU38 2.5 45.8 1.0
O F:ILE30 2.6 40.2 1.0
O F:SER27 2.6 41.4 1.0
CD E:GLU38 3.4 42.7 1.0
OE1 E:GLU38 3.5 42.9 1.0
C F:SER27 3.7 42.9 1.0
OD2 F:ASP59 3.8 57.9 1.0
C F:ILE30 3.8 41.0 1.0
O F:HIS58 4.0 39.8 1.0
O F:HOH506 4.1 41.5 1.0
OG F:SER27 4.1 49.6 1.0
O F:LEU28 4.2 42.6 1.0
CA F:LEU28 4.2 42.5 1.0
C F:LEU28 4.4 43.8 1.0
N F:LEU28 4.4 43.5 1.0
N F:PHE32 4.4 36.4 1.0
C F:PRO31 4.6 36.1 1.0
N F:ILE30 4.6 43.7 1.0
CA F:ILE30 4.7 42.7 1.0
CG F:ASP59 4.7 52.6 1.0
CA F:SER27 4.7 44.4 1.0
CA F:PRO31 4.7 40.7 1.0
N F:PRO31 4.8 43.1 1.0
CG E:GLU38 4.8 40.9 1.0
CB F:ILE30 4.8 43.1 1.0
CA F:PHE32 4.9 38.3 1.0

Reference:

M.Grzechowiak, J.Sliwiak, M.Jaskolski, M.Ruszkowski. Structural Studies of Glutamate Dehydrogenase (Isoform 1) From Arabidopsis Thaliana, An Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism To Be Published.
Page generated: Mon Aug 12 18:26:28 2024

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