Calcium 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:

Sodium (Na) 3 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 8owm

Go back to Calcium Binding Sites List in 8owm
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca510

b:17.4
occ:1.00
 O A:ILE30 2.2 19.0 1.0
OE1 F:GLU38 2.3 24.0 1.0
O A:HOH686 2.3 22.2 1.0
O A:SER27 2.3 22.7 1.0
O F:HOH797 2.4 24.0 1.0
O A:HOH693 2.4 18.9 1.0
CD F:GLU38 3.4 22.1 1.0
C A:SER27 3.5 21.6 1.0
C A:ILE30 3.5 19.6 1.0
OG A:SER27 3.9 20.4 1.0
OE2 F:GLU38 4.0 23.4 1.0
CA A:LEU28 4.2 19.6 1.0
O A:HIS58 4.2 18.9 1.0
CA A:ILE30 4.2 18.4 1.0
N A:ILE30 4.3 19.5 1.0
N A:LEU28 4.3 20.9 1.0
N A:PHE32 4.3 17.5 1.0
CB A:ILE30 4.3 19.4 1.0
C A:LEU28 4.3 19.4 1.0
C A:PRO31 4.3 19.6 1.0
OD2 A:ASP59 4.4 24.8 1.0
CA A:SER27 4.4 19.3 1.0
O A:LEU28 4.4 21.6 1.0
N A:PRO31 4.4 22.2 1.0
CA A:PRO31 4.5 21.3 1.0
O A:HOH627 4.6 21.8 1.0
O A:HOH833 4.6 25.5 1.0
CG F:GLU38 4.6 22.4 1.0
CB F:GLU38 4.7 20.7 1.0
O A:PRO31 4.8 19.3 1.0
CB A:SER27 4.8 20.3 1.0
O F:HOH705 4.8 25.5 1.0
CA A:PHE32 4.9 19.6 1.0
C A:MET29 5.0 23.5 0.5
CG2 A:ILE30 5.0 21.8 1.0
C A:MET29 5.0 23.5 0.5
N A:MET29 5.0 19.9 0.5

Calcium binding site 2 out of 6 in 8owm

Go back to Calcium Binding Sites List in 8owm
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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:Ca515

b:22.2
occ:1.00
 OE1 E:GLU38 2.3 25.2 1.0
O B:SER27 2.3 23.8 1.0
O B:ILE30 2.3 23.4 1.0
O E:HOH4524 2.4 26.9 1.0
O B:HOH725 2.4 23.5 1.0
O B:HOH643 2.4 25.0 1.0
C B:SER27 3.4 24.9 1.0
CD E:GLU38 3.4 28.4 1.0
C B:ILE30 3.5 23.9 1.0
OG B:SER27 4.0 24.2 1.0
OE2 E:GLU38 4.0 25.1 1.0
CA B:LEU28 4.2 22.9 1.0
N B:LEU28 4.2 27.0 1.0
O B:HIS58 4.3 20.4 1.0
O B:LEU28 4.3 23.6 1.0
C B:LEU28 4.3 25.4 1.0
CA B:ILE30 4.3 22.9 1.0
N B:ILE30 4.3 25.0 1.0
N B:PHE32 4.3 18.8 1.0
CA B:SER27 4.4 25.5 1.0
CB B:ILE30 4.4 22.9 1.0
OD2 B:ASP59 4.4 26.8 1.0
C B:PRO31 4.4 22.6 1.0
N B:PRO31 4.5 27.2 1.0
O B:HOH785 4.6 24.2 1.0
O B:HOH644 4.6 26.3 1.0
CG E:GLU38 4.6 22.1 1.0
CA B:PRO31 4.6 23.1 1.0
CB E:GLU38 4.8 21.3 1.0
O B:PRO31 4.8 23.1 1.0
CB B:SER27 4.8 24.7 1.0
O E:HOH4447 4.9 28.8 1.0
CA B:PHE32 4.9 20.4 1.0
C B:MET29 5.0 25.1 1.0
CG2 B:ILE30 5.0 24.1 1.0
N B:MET29 5.0 26.8 1.0

Calcium binding site 3 out of 6 in 8owm

Go back to Calcium Binding Sites List in 8owm
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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:Ca513

b:20.4
occ:1.00
 OE1 D:GLU38 2.3 23.0 1.0
O D:HOH779 2.3 26.2 1.0
O C:ILE30 2.3 23.1 1.0
O C:SER27 2.3 21.7 1.0
O C:HOH638 2.3 25.7 1.0
O C:HOH700 2.4 21.8 1.0
C C:SER27 3.4 21.2 1.0
CD D:GLU38 3.5 24.3 1.0
C C:ILE30 3.5 25.5 1.0
OG C:SER27 3.9 23.2 1.0
OE2 D:GLU38 4.0 22.7 1.0
CA C:LEU28 4.2 23.5 1.0
N C:LEU28 4.2 20.2 1.0
N C:ILE30 4.3 21.4 1.0
CA C:ILE30 4.3 20.0 1.0
O C:HIS58 4.3 17.9 1.0
N C:PHE32 4.3 20.8 1.0
OD2 C:ASP59 4.3 26.3 1.0
C C:LEU28 4.3 23.6 1.0
C C:PRO31 4.3 22.1 1.0
CA C:SER27 4.4 21.2 1.0
O C:LEU28 4.4 22.6 1.0
CB C:ILE30 4.4 21.7 1.0
N C:PRO31 4.5 23.8 1.0
O C:HOH628 4.6 23.4 1.0
CA C:PRO31 4.6 22.3 1.0
O C:HOH836 4.6 25.4 1.0
CG D:GLU38 4.6 21.9 1.0
CB D:GLU38 4.7 21.5 1.0
O C:PRO31 4.7 21.4 1.0
O D:HOH716 4.8 27.0 1.0
CB C:SER27 4.8 22.0 1.0
CA C:PHE32 4.9 19.6 1.0
C C:MET29 4.9 24.7 0.4
C C:MET29 4.9 24.8 0.6
N C:MET29 5.0 21.2 0.6
N C:MET29 5.0 21.2 0.4

Calcium binding site 4 out of 6 in 8owm

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Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca binding site number 4 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
D:Ca507

b:21.5
occ:1.00
 OE1 C:GLU38 2.2 26.1 1.0
O D:ILE30 2.3 22.8 1.0
O D:SER27 2.3 24.6 1.0
O D:HOH610 2.4 26.1 1.0
O C:HOH837 2.4 24.7 1.0
O D:HOH651 2.4 22.0 1.0
CD C:GLU38 3.4 23.4 1.0
C D:SER27 3.4 24.0 1.0
C D:ILE30 3.5 26.6 1.0
OG D:SER27 3.9 24.3 1.0
OE2 C:GLU38 3.9 24.5 1.0
CA D:LEU28 4.2 25.6 1.0
CA D:ILE30 4.3 24.5 1.0
O D:HIS58 4.3 21.7 1.0
N D:PHE32 4.3 20.9 1.0
N D:LEU28 4.3 26.6 1.0
N D:ILE30 4.3 25.8 1.0
OD2 D:ASP59 4.3 27.3 1.0
C D:PRO31 4.3 21.4 1.0
C D:LEU28 4.3 24.8 1.0
CA D:SER27 4.4 24.6 1.0
CB D:ILE30 4.4 24.7 1.0
O D:LEU28 4.4 26.6 1.0
N D:PRO31 4.5 25.9 1.0
CA D:PRO31 4.6 24.9 1.0
CG C:GLU38 4.6 23.6 1.0
O D:HOH782 4.6 24.8 1.0
O D:HOH636 4.6 23.4 1.0
CB C:GLU38 4.7 21.6 1.0
O D:PRO31 4.7 23.6 1.0
CB D:SER27 4.7 25.8 1.0
O C:HOH766 4.7 27.0 1.0
CA D:PHE32 4.9 21.3 1.0
C D:MET29 5.0 29.4 0.6
C D:MET29 5.0 29.3 0.4
CG2 D:ILE30 5.0 26.6 1.0

Calcium binding site 5 out of 6 in 8owm

Go back to Calcium Binding Sites List in 8owm
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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
E:Ca4211

b:19.9
occ:1.00
 O E:ILE30 2.2 22.3 1.0
OE1 B:GLU38 2.2 22.9 1.0
O E:HOH4377 2.3 23.4 1.0
O E:HOH4356 2.3 20.9 1.0
O E:SER27 2.3 23.6 1.0
O B:HOH806 2.4 24.4 1.0
C E:SER27 3.4 23.0 1.0
CD B:GLU38 3.4 26.2 1.0
C E:ILE30 3.5 22.1 1.0
OG E:SER27 3.9 23.7 1.0
OE2 B:GLU38 4.0 24.6 1.0
CA E:LEU28 4.2 24.4 1.0
N E:ILE30 4.2 21.6 1.0
CA E:ILE30 4.2 22.1 1.0
N E:LEU28 4.2 24.3 1.0
O E:HIS58 4.2 20.6 1.0
N E:PHE32 4.3 21.0 1.0
C E:PRO31 4.3 20.1 1.0
OD2 E:ASP59 4.4 27.9 1.0
CB E:ILE30 4.4 21.6 1.0
C E:LEU28 4.4 24.1 1.0
CA E:SER27 4.4 22.9 1.0
O E:LEU28 4.4 25.1 1.0
N E:PRO31 4.5 23.7 1.0
CA E:PRO31 4.5 23.6 1.0
O E:HOH4515 4.6 26.5 1.0
O E:HOH4317 4.6 22.5 1.0
CG B:GLU38 4.6 22.9 1.0
O E:PRO31 4.7 20.3 1.0
CB B:GLU38 4.7 21.5 1.0
CB E:SER27 4.8 22.3 1.0
O B:HOH759 4.8 25.6 1.0
CA E:PHE32 4.9 21.1 1.0
C E:MET29 4.9 26.5 1.0

Calcium binding site 6 out of 6 in 8owm

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Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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
F:Ca507

b:19.6
occ:1.00
 O F:SER27 2.2 23.0 1.0
O A:HOH806 2.3 26.5 1.0
O F:ILE30 2.3 23.7 1.0
OE1 A:GLU38 2.3 25.5 1.0
O F:HOH667 2.3 22.3 1.0
O F:HOH620 2.3 23.5 1.0
C F:SER27 3.4 20.8 1.0
CD A:GLU38 3.5 22.7 1.0
C F:ILE30 3.5 25.4 1.0
OG F:SER27 3.9 22.9 1.0
OE2 A:GLU38 4.0 23.8 1.0
CA F:LEU28 4.2 21.2 1.0
N F:LEU28 4.2 22.9 1.0
O F:HIS58 4.2 21.2 1.0
CA F:ILE30 4.2 21.9 1.0
N F:ILE30 4.2 23.4 1.0
O F:LEU28 4.3 24.9 1.0
C F:LEU28 4.3 25.0 1.0
OD2 F:ASP59 4.3 26.4 1.0
CA F:SER27 4.3 21.7 1.0
N F:PHE32 4.4 19.9 1.0
C F:PRO31 4.4 18.6 1.0
CB F:ILE30 4.4 19.9 1.0
N F:PRO31 4.5 21.2 1.0
CA F:PRO31 4.6 19.8 1.0
O F:HOH634 4.6 21.0 1.0
O F:HOH770 4.6 23.6 1.0
CG A:GLU38 4.7 22.1 1.0
O3 A:GOL509 4.8 26.2 1.0
CB F:SER27 4.8 21.8 1.0
CB A:GLU38 4.8 22.6 1.0
O F:PRO31 4.8 20.4 1.0
C F:MET29 4.9 24.0 1.0
CA F:PHE32 4.9 21.3 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: Fri Jul 19 11:04:04 2024

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