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Calcium in PDB 8own: Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form

Enzymatic activity of Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form

All present enzymatic activity of Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form:
1.4.1.3;

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form (pdb code 8own). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form, PDB code: 8own:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8own

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Calcium binding site 1 out of 6 in the Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:32.0
occ:1.00
 O A:SER27 2.6 44.6 1.0
O A:ILE30 2.6 35.7 1.0
OE1 D:GLU38 2.8 34.9 1.0
OD1 A:ASP59 3.3 32.2 1.0
CD D:GLU38 3.7 34.9 1.0
C A:SER27 3.8 44.6 1.0
C A:ILE30 3.9 35.7 1.0
OE2 D:GLU38 4.0 34.9 1.0
OG A:SER27 4.2 44.6 1.0
CA A:LEU28 4.4 40.2 1.0
O A:HIS58 4.4 29.4 1.0
CG A:ASP59 4.4 32.2 1.0
N A:LEU28 4.5 40.2 1.0
N A:ILE30 4.6 35.7 1.0
CA A:ILE30 4.6 35.7 1.0
C A:LEU28 4.7 40.2 1.0
C A:PRO31 4.7 30.8 1.0
N A:PHE32 4.7 27.9 1.0
CA A:SER27 4.8 44.6 1.0
CB A:ILE30 4.8 35.7 1.0
N A:PRO31 4.8 30.8 1.0
O A:LEU28 4.8 40.2 1.0
CA A:PRO31 4.8 30.8 1.0
OD2 A:ASP59 4.9 32.2 1.0
CG D:GLU38 5.0 34.9 1.0
O A:PRO31 5.0 30.8 1.0

Calcium binding site 2 out of 6 in 8own

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Calcium binding site 2 out of 6 in the Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:31.5
occ:1.00
 O B:SER27 2.6 46.3 1.0
O B:ILE30 2.6 36.7 1.0
OE1 E:GLU38 3.1 35.0 1.0
OD1 B:ASP59 3.3 33.1 1.0
C B:SER27 3.8 46.3 1.0
C B:ILE30 3.9 36.7 1.0
CD E:GLU38 4.0 35.0 1.0
OE2 E:GLU38 4.2 35.0 1.0
OG B:SER27 4.2 46.3 1.0
CA B:LEU28 4.4 41.0 1.0
O B:HIS58 4.4 29.6 1.0
CG B:ASP59 4.4 33.1 1.0
N B:LEU28 4.5 41.0 1.0
N B:ILE30 4.6 36.7 1.0
CA B:ILE30 4.6 36.7 1.0
C B:PRO31 4.7 31.4 1.0
C B:LEU28 4.7 41.0 1.0
N B:PHE32 4.7 28.2 1.0
CA B:SER27 4.8 46.3 1.0
CB B:ILE30 4.8 36.7 1.0
N B:PRO31 4.8 31.4 1.0
CA B:PRO31 4.8 31.4 1.0
O B:LEU28 4.8 41.0 1.0
OD2 B:ASP59 4.9 33.1 1.0
O B:PRO31 5.0 31.4 1.0

Calcium binding site 3 out of 6 in 8own

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Calcium binding site 3 out of 6 in the Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:33.0
occ:1.00
 O C:SER27 2.6 46.1 1.0
O C:ILE30 2.6 37.7 1.0
OE1 F:GLU38 2.8 36.9 1.0
OD1 C:ASP59 3.4 34.5 1.0
CD F:GLU38 3.7 36.9 1.0
C C:SER27 3.8 46.1 1.0
C C:ILE30 3.9 37.7 1.0
OE2 F:GLU38 4.1 36.9 1.0
OG C:SER27 4.2 46.1 1.0
O C:HIS58 4.4 30.4 1.0
CA C:LEU28 4.5 40.8 1.0
CG C:ASP59 4.5 34.5 1.0
C C:PRO31 4.6 32.5 1.0
N C:ILE30 4.6 37.7 1.0
N C:LEU28 4.6 40.8 1.0
CA C:ILE30 4.6 37.7 1.0
N C:PHE32 4.7 28.9 1.0
CB C:ILE30 4.8 37.7 1.0
CA C:SER27 4.8 46.1 1.0
C C:LEU28 4.8 40.8 1.0
N C:PRO31 4.8 32.5 1.0
CA C:PRO31 4.8 32.5 1.0
O C:PRO31 4.9 32.5 1.0
CG F:GLU38 5.0 36.9 1.0
O C:LEU28 5.0 40.8 1.0

Calcium binding site 4 out of 6 in 8own

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Calcium binding site 4 out of 6 in the Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:30.0
occ:1.00
 O D:SER27 2.5 47.6 1.0
O D:ILE30 2.7 36.9 1.0
OE1 A:GLU38 3.1 35.2 1.0
OD1 D:ASP59 3.2 35.4 1.0
C D:SER27 3.7 47.6 1.0
C D:ILE30 3.9 36.9 1.0
CD A:GLU38 4.0 35.2 1.0
OG D:SER27 4.2 47.6 1.0
CA D:LEU28 4.3 43.4 1.0
OE2 A:GLU38 4.3 35.2 1.0
CG D:ASP59 4.3 35.4 1.0
O D:HIS58 4.4 31.6 1.0
N D:LEU28 4.4 43.4 1.0
N D:ILE30 4.6 36.9 1.0
C D:LEU28 4.6 43.4 1.0
CA D:ILE30 4.7 36.9 1.0
C D:PRO31 4.7 30.8 1.0
O D:LEU28 4.7 43.4 1.0
N D:PHE32 4.8 29.6 1.0
CA D:SER27 4.8 47.6 1.0
OD2 D:ASP59 4.8 35.4 1.0
N D:PRO31 4.8 30.8 1.0
CB D:ILE30 4.9 36.9 1.0
CA D:PRO31 4.9 30.8 1.0

Calcium binding site 5 out of 6 in 8own

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Calcium binding site 5 out of 6 in the Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca501

b:31.1
occ:1.00
 O E:SER27 2.6 46.7 1.0
O E:ILE30 2.6 37.2 1.0
OE1 B:GLU38 3.0 36.1 1.0
OD1 E:ASP59 3.3 36.3 1.0
C E:SER27 3.7 46.7 1.0
C E:ILE30 3.8 37.2 1.0
CD B:GLU38 3.9 36.1 1.0
OE2 B:GLU38 4.2 36.1 1.0
OG E:SER27 4.2 46.7 1.0
CA E:LEU28 4.4 43.8 1.0
O E:HIS58 4.4 31.8 1.0
CG E:ASP59 4.5 36.3 1.0
N E:LEU28 4.5 43.8 1.0
N E:ILE30 4.5 37.2 1.0
CA E:ILE30 4.6 37.2 1.0
C E:PRO31 4.6 32.0 1.0
C E:LEU28 4.7 43.8 1.0
N E:PHE32 4.7 31.0 1.0
CA E:SER27 4.8 46.7 1.0
CB E:ILE30 4.8 37.2 1.0
N E:PRO31 4.8 32.0 1.0
CA E:PRO31 4.8 32.0 1.0
O E:LEU28 4.9 43.8 1.0
OD2 E:ASP59 4.9 36.3 1.0
O E:PRO31 5.0 32.0 1.0

Calcium binding site 6 out of 6 in 8own

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Calcium binding site 6 out of 6 in the Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryoem Structure of Glutamate Dehydrogenase Isoform 2 From Arabidopsis Thaliana in Apo-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca501

b:33.6
occ:1.00
 O F:SER27 2.4 48.3 1.0
O F:ILE30 2.8 38.4 1.0
OE1 C:GLU38 3.2 36.3 1.0
OD1 F:ASP59 3.2 35.5 1.0
C F:SER27 3.6 48.3 1.0
C F:ILE30 4.0 38.4 1.0
OG F:SER27 4.1 48.3 1.0
CD C:GLU38 4.1 36.3 1.0
CA F:LEU28 4.2 44.0 1.0
N F:LEU28 4.3 44.0 1.0
OE2 C:GLU38 4.3 36.3 1.0
CG F:ASP59 4.3 35.5 1.0
O F:HIS58 4.5 31.1 1.0
C F:LEU28 4.5 44.0 1.0
N F:ILE30 4.6 38.4 1.0
CA F:SER27 4.6 48.3 1.0
O F:LEU28 4.7 44.0 1.0
CA F:ILE30 4.7 38.4 1.0
OD2 F:ASP59 4.8 35.5 1.0
C F:PRO31 4.9 32.3 1.0
CB F:ILE30 4.9 38.4 1.0
N F:PHE32 4.9 30.6 1.0
CD2 F:LEU28 5.0 44.0 1.0
N F:PRO31 5.0 32.3 1.0
CB F:SER27 5.0 48.3 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: Thu Dec 28 01:43:35 2023

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