Potassium in PDB 6yei: Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad

Enzymatic activity of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad

All present enzymatic activity of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad:
1.4.1.3;

Protein crystallography data

The structure of Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad, PDB code: 6yei 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) 70.26 / 2.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.843, 99.811, 317.948, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.6

Potassium Binding Sites:

The binding sites of Potassium atom in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad (pdb code 6yei). 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 Complex with Nad, PDB code: 6yei:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 6yei

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Potassium binding site 1 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad


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 Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K506

b:31.1
occ:1.00
 O A:ILE30 2.4 27.9 1.0
O A:HOH608 2.4 34.9 1.0
OE1 B:GLU38 2.4 30.9 1.0
O A:SER27 2.4 31.4 1.0
O A:HOH702 2.5 28.5 1.0
O B:HOH721 2.6 44.4 1.0
CD B:GLU38 3.5 35.5 1.0
C A:SER27 3.5 28.3 1.0
C A:ILE30 3.6 30.1 1.0
OE2 B:GLU38 3.9 41.0 1.0
OG A:SER27 4.1 33.2 1.0
CA A:LEU28 4.1 28.3 1.0
O A:LEU28 4.1 30.1 1.0
C A:LEU28 4.2 27.2 1.0
N A:ILE30 4.2 31.4 1.0
OD2 A:ASP59 4.2 39.2 1.0
N A:LEU28 4.2 30.0 1.0
O A:HIS58 4.3 30.0 1.0
CA A:ILE30 4.3 25.5 1.0
N A:PHE32 4.3 24.8 1.0
C A:PRO31 4.4 26.1 1.0
CB A:ILE30 4.5 29.5 1.0
CA A:SER27 4.5 28.8 1.0
N A:PRO31 4.5 28.9 1.0
CA A:PRO31 4.6 24.8 1.0
O A:HOH619 4.6 33.9 1.0
CG B:GLU38 4.7 26.7 1.0
N A:LEU29 4.8 28.1 1.0
CB B:GLU38 4.9 24.4 1.0
C A:LEU29 4.9 37.3 1.0
O B:HOH673 4.9 43.6 1.0
O A:HOH697 4.9 35.3 1.0
O A:PRO31 4.9 27.6 1.0
CB A:SER27 5.0 31.7 1.0
CA A:PHE32 5.0 25.7 1.0

Potassium binding site 2 out of 6 in 6yei

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Potassium binding site 2 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad


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 Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K507

b:37.9
occ:1.00
 OE1 A:GLU38 2.3 36.0 1.0
O B:ILE30 2.4 27.0 1.0
O B:HOH644 2.4 42.8 1.0
O B:HOH682 2.4 34.6 1.0
O B:SER27 2.5 29.6 1.0
O B:HOH712 2.5 36.0 1.0
CD A:GLU38 3.3 45.7 1.0
C B:SER27 3.5 34.3 1.0
C B:ILE30 3.5 25.9 1.0
OE2 A:GLU38 3.8 48.3 1.0
OG B:SER27 4.0 42.0 1.0
CA B:LEU28 4.1 33.7 1.0
N B:ILE30 4.2 33.7 1.0
C B:LEU28 4.2 38.4 1.0
CA B:ILE30 4.2 34.8 1.0
O B:LEU28 4.3 36.8 1.0
N B:LEU28 4.3 33.4 1.0
O B:HIS58 4.3 32.2 1.0
CB B:ILE30 4.4 33.1 1.0
OD2 B:ASP59 4.4 45.2 1.0
N B:PHE32 4.4 29.4 1.0
C B:PRO31 4.5 30.6 1.0
CA B:SER27 4.5 37.1 1.0
N B:PRO31 4.6 27.0 1.0
CG A:GLU38 4.6 39.9 1.0
O B:HOH604 4.6 35.3 1.0
CA B:PRO31 4.7 28.0 1.0
CB A:GLU38 4.8 37.1 1.0
N B:LEU29 4.9 34.6 1.0
CB B:SER27 4.9 32.7 1.0
C B:LEU29 4.9 41.0 1.0
O B:PRO31 5.0 29.8 1.0
CG2 B:ILE30 5.0 24.7 1.0

Potassium binding site 3 out of 6 in 6yei

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Potassium binding site 3 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad


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 Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K505

b:45.9
occ:1.00
 OE2 D:GLU38 2.4 45.0 1.0
O C:SER27 2.4 40.0 1.0
O C:ILE30 2.4 37.0 1.0
O C:HOH663 2.5 49.2 1.0
O C:HOH676 2.5 33.2 1.0
O C:HOH689 2.6 47.3 1.0
CD D:GLU38 3.4 51.8 1.0
C C:SER27 3.5 46.2 1.0
C C:ILE30 3.6 43.2 1.0
OE1 D:GLU38 3.8 56.6 1.0
OG C:SER27 4.0 45.7 1.0
CA C:LEU28 4.1 46.8 1.0
C C:LEU28 4.2 45.4 1.0
O C:LEU28 4.2 48.2 1.0
N C:LEU28 4.2 43.0 1.0
O C:HIS58 4.2 34.8 1.0
N C:ILE30 4.2 41.7 1.0
OD2 C:ASP59 4.3 50.2 1.0
CA C:ILE30 4.3 39.1 1.0
O C:HOH604 4.4 36.0 1.0
N C:PHE32 4.4 33.6 1.0
CB C:ILE30 4.5 34.2 1.0
CA C:SER27 4.5 44.5 1.0
O D:HOH696 4.5 54.6 1.0
C C:PRO31 4.6 37.9 1.0
N C:PRO31 4.7 35.3 1.0
CG D:GLU38 4.7 41.4 1.0
CA C:PRO31 4.7 33.7 1.0
O C:HOH664 4.8 45.3 1.0
N C:LEU29 4.9 45.7 1.0
CB C:SER27 4.9 43.2 1.0
CB D:GLU38 4.9 35.7 1.0
C C:LEU29 5.0 45.5 1.0

Potassium binding site 4 out of 6 in 6yei

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Potassium binding site 4 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad


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 Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K507

b:38.6
occ:1.00
 O D:ILE30 2.4 30.6 1.0
OE2 C:GLU38 2.4 43.1 1.0
O D:SER27 2.4 33.5 1.0
O D:HOH677 2.5 31.0 1.0
O D:HOH602 2.5 45.9 1.0
O D:HOH704 2.5 39.9 1.0
CD C:GLU38 3.4 43.7 1.0
C D:SER27 3.5 36.6 1.0
C D:ILE30 3.6 35.4 1.0
OE1 C:GLU38 3.7 49.6 1.0
OG D:SER27 4.0 38.0 1.0
CA D:LEU28 4.1 34.6 1.0
O D:LEU28 4.1 42.1 1.0
C D:LEU28 4.1 40.3 1.0
N D:ILE30 4.1 40.0 1.0
N D:LEU28 4.2 35.0 1.0
CA D:ILE30 4.2 39.7 1.0
O D:HIS58 4.3 28.9 1.0
OD2 D:ASP59 4.4 39.9 1.0
N D:PHE32 4.4 27.7 1.0
CB D:ILE30 4.4 38.1 1.0
O C:HOH681 4.4 49.3 1.0
CA D:SER27 4.5 29.7 1.0
C D:PRO31 4.5 31.0 1.0
O D:HOH603 4.5 33.8 1.0
N D:PRO31 4.6 32.0 1.0
CG C:GLU38 4.7 38.0 1.0
CA D:PRO31 4.7 31.0 1.0
O D:HOH682 4.8 35.5 1.0
N D:LEU29 4.9 35.8 1.0
CB C:GLU38 4.9 29.0 1.0
C D:LEU29 4.9 40.6 1.0
CB D:SER27 4.9 29.9 1.0
O D:PRO31 5.0 35.1 1.0

Potassium binding site 5 out of 6 in 6yei

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Potassium binding site 5 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad


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 Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K504

b:43.4
occ:1.00
 O E:SER27 2.4 33.6 1.0
OE1 F:GLU38 2.4 43.0 1.0
O E:ILE30 2.4 32.5 1.0
O E:HOH619 2.5 41.5 1.0
O E:HOH647 2.6 36.7 1.0
O F:HOH732 2.7 50.7 1.0
CD F:GLU38 3.4 44.0 1.0
C E:SER27 3.5 34.0 1.0
C E:ILE30 3.6 32.6 1.0
OE2 F:GLU38 3.8 50.0 1.0
OG E:SER27 4.0 39.0 1.0
CA E:LEU28 4.1 38.3 1.0
O E:LEU28 4.1 44.9 1.0
C E:LEU28 4.1 39.4 1.0
O E:HIS58 4.2 30.2 1.0
N E:ILE30 4.2 43.2 1.0
N E:LEU28 4.2 36.5 1.0
N E:PHE32 4.3 32.5 1.0
CA E:ILE30 4.3 41.6 1.0
OD2 E:ASP59 4.4 39.0 1.0
C E:PRO31 4.4 34.3 1.0
CB E:ILE30 4.5 36.9 1.0
CA E:SER27 4.5 39.5 1.0
N E:PRO31 4.6 33.5 1.0
O E:HOH617 4.7 37.3 1.0
CA E:PRO31 4.7 35.4 1.0
CG F:GLU38 4.7 37.4 1.0
N E:LEU29 4.8 38.9 1.0
O F:HOH699 4.9 50.3 1.0
O E:PRO31 4.9 31.9 1.0
O E:HOH639 4.9 42.2 1.0
CA E:PHE32 4.9 31.9 1.0
C E:LEU29 4.9 44.8 1.0
CB E:SER27 4.9 37.2 1.0
CB F:GLU38 5.0 30.0 1.0

Potassium binding site 6 out of 6 in 6yei

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Potassium binding site 6 out of 6 in the Arabidopsis Thaliana Glutamate Dehydrogenase Isoform 1 in Complex with Nad


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 Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K506

b:40.2
occ:1.00
 O F:ILE30 2.4 35.8 1.0
OE1 E:GLU38 2.4 41.4 1.0
O F:SER27 2.5 35.8 1.0
O F:HOH628 2.5 38.0 1.0
O F:HOH688 2.5 36.9 1.0
O F:HOH725 2.6 43.3 1.0
CD E:GLU38 3.4 43.6 1.0
C F:SER27 3.5 35.6 1.0
C F:ILE30 3.5 39.1 1.0
OE2 E:GLU38 3.8 45.6 1.0
OG F:SER27 4.1 42.0 1.0
O F:LEU28 4.1 39.7 1.0
CA F:LEU28 4.1 35.0 1.0
O F:HIS58 4.2 28.7 1.0
C F:LEU28 4.2 39.4 1.0
N F:ILE30 4.2 32.9 1.0
OD2 F:ASP59 4.3 42.5 1.0
N F:PHE32 4.3 26.8 1.0
CA F:ILE30 4.3 35.8 1.0
N F:LEU28 4.3 30.7 1.0
CB F:ILE30 4.4 34.5 1.0
C F:PRO31 4.4 32.5 1.0
CA F:SER27 4.5 35.6 1.0
N F:PRO31 4.5 34.3 1.0
O F:HOH601 4.6 36.0 1.0
CA F:PRO31 4.6 31.5 1.0
CG E:GLU38 4.7 39.9 1.0
N F:LEU29 4.9 37.6 1.0
CA F:PHE32 4.9 32.4 1.0
CB E:GLU38 4.9 37.8 1.0
C F:LEU29 4.9 38.1 1.0
O F:PRO31 4.9 34.6 1.0
O F:HOH660 4.9 41.8 1.0
CB F:SER27 4.9 37.2 1.0
CG2 F:ILE30 5.0 32.7 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 Dec 14 02:29:22 2020

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