Potassium in PDB 8ar7: Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine

Enzymatic activity of Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine

All present enzymatic activity of Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine:
1.4.1.3;

Protein crystallography data

The structure of Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine, PDB code: 8ar7 was solved by V.A.Aleshin, M.Bellinzoni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 120.20 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.877, 178.705, 123.884, 90, 104, 90
R / Rfree (%) 19.2 / 21.5

Potassium Binding Sites:

The binding sites of Potassium atom in the Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine (pdb code 8ar7). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine, PDB code: 8ar7:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 8ar7

Go back to Potassium Binding Sites List in 8ar7
Potassium binding site 1 out of 6 in the Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:47.7
occ:1.00
 O A:HOH718 2.4 32.9 1.0
O A:PRO114 2.6 50.5 1.0
OD1 A:ASN116 2.7 50.2 1.0
O A:ILE111 2.8 55.5 1.0
O A:HIS142 2.9 45.1 1.0
O A:ILE112 3.2 52.9 1.0
CG A:ASN116 3.4 49.0 1.0
O A:HOH720 3.6 47.1 1.0
C A:ILE112 3.7 52.7 1.0
CA A:ILE112 3.8 53.2 1.0
C A:ILE111 3.8 55.2 1.0
ND2 A:ASN116 3.8 48.9 1.0
C A:PRO114 3.9 50.2 1.0
C A:HIS142 4.1 45.2 1.0
N A:ASN116 4.2 47.7 1.0
N A:ILE112 4.2 53.9 1.0
NE2 A:HIS142 4.3 53.9 1.0
OH A:TYR553 4.4 59.9 1.0
CA A:SER143 4.4 45.1 1.0
CB A:SER143 4.5 47.1 1.0
CB A:ASN116 4.5 47.0 1.0
CD2 A:HIS142 4.5 52.5 1.0
N A:PRO114 4.5 50.5 1.0
CE1 A:HIS142 4.6 53.7 1.0
C A:CYS115 4.6 49.0 1.0
CD A:PRO114 4.6 49.9 1.0
CA A:ASN116 4.7 46.9 1.0
OG A:SER143 4.7 49.8 1.0
CA A:CYS115 4.7 50.0 1.0
N A:LYS113 4.8 52.0 1.0
N A:CYS115 4.8 49.9 1.0
N A:SER143 4.8 44.9 1.0
CA A:PRO114 4.8 50.2 1.0
CG2 A:ILE111 4.9 57.5 1.0
CG A:HIS142 4.9 50.8 1.0
ND1 A:HIS142 4.9 52.8 1.0
C A:LYS113 4.9 51.2 1.0
CG A:PRO114 5.0 51.3 1.0

Potassium binding site 2 out of 6 in 8ar7

Go back to Potassium Binding Sites List in 8ar7
Potassium binding site 2 out of 6 in the Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:53.6
occ:1.00
 O B:PRO114 2.4 56.4 1.0
O B:HOH733 2.5 28.6 1.0
O B:HIS142 2.8 50.1 1.0
O B:ILE112 2.8 54.0 1.0
OD1 B:ASN116 2.8 58.9 1.0
O B:ILE111 2.9 55.8 1.0
CG B:ASN116 3.5 57.9 1.0
C B:PRO114 3.6 55.6 1.0
C B:ILE112 3.6 53.9 1.0
ND2 B:ASN116 3.8 58.5 1.0
C B:HIS142 3.9 49.8 1.0
N B:ASN116 4.0 54.5 1.0
CA B:ILE112 4.0 54.1 1.0
C B:ILE111 4.0 55.4 1.0
NE2 B:HIS142 4.0 55.2 1.0
CD2 B:HIS142 4.1 53.8 1.0
CE1 B:HIS142 4.3 55.2 1.0
N B:PRO114 4.3 54.6 1.0
C B:CYS115 4.4 55.0 1.0
CA B:SER143 4.4 49.1 1.0
CA B:CYS115 4.4 55.2 1.0
N B:ILE112 4.5 54.4 1.0
CB B:ASN116 4.5 55.0 1.0
N B:CYS115 4.5 55.2 1.0
CB B:SER143 4.5 50.0 1.0
CA B:PRO114 4.5 54.8 1.0
CG B:HIS142 4.6 52.6 1.0
CA B:ASN116 4.6 54.2 1.0
CD B:PRO114 4.6 54.1 1.0
N B:SER143 4.6 49.2 1.0
ND1 B:HIS142 4.6 54.5 1.0
C B:LYS113 4.7 54.8 1.0
N B:LYS113 4.7 53.8 1.0
CG B:PRO114 4.7 55.6 1.0
OH B:TYR553 4.8 60.7 1.0
CA B:HIS142 4.9 49.7 1.0
OG B:SER143 4.9 52.0 1.0
O B:LYS113 5.0 55.1 1.0

Potassium binding site 3 out of 6 in 8ar7

Go back to Potassium Binding Sites List in 8ar7
Potassium binding site 3 out of 6 in the Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:46.2
occ:1.00
 O C:HOH710 2.5 54.4 1.0
O C:PRO114 2.5 44.7 1.0
OD1 C:ASN116 2.6 48.1 1.0
O C:ILE111 2.8 42.7 1.0
O C:ILE112 2.9 41.7 1.0
O C:HIS142 2.9 39.1 1.0
O C:HOH708 3.3 47.5 1.0
CG C:ASN116 3.4 47.1 1.0
C C:ILE112 3.6 41.8 1.0
C C:PRO114 3.7 44.0 1.0
CA C:ILE112 3.8 41.5 1.0
ND2 C:ASN116 3.9 48.3 1.0
C C:ILE111 3.9 42.4 1.0
N C:ASN116 4.0 43.0 1.0
C C:HIS142 4.1 38.5 1.0
NE2 C:HIS142 4.1 43.0 1.0
CD2 C:HIS142 4.2 41.8 1.0
N C:ILE112 4.3 41.9 1.0
N C:PRO114 4.4 43.2 1.0
C C:CYS115 4.5 43.3 1.0
CE1 C:HIS142 4.5 42.7 1.0
CB C:ASN116 4.5 43.9 1.0
CA C:SER143 4.6 37.8 1.0
CA C:ASN116 4.6 43.1 1.0
CD C:PRO114 4.6 42.6 1.0
CA C:CYS115 4.6 43.6 1.0
CB C:SER143 4.6 38.8 1.0
N C:CYS115 4.6 43.5 1.0
OH C:TYR553 4.6 55.7 1.0
CA C:PRO114 4.6 43.4 1.0
N C:LYS113 4.7 42.0 1.0
CG C:HIS142 4.7 40.4 1.0
CG C:PRO114 4.8 44.0 1.0
C C:LYS113 4.8 43.3 1.0
N C:SER143 4.8 37.9 1.0
ND1 C:HIS142 4.9 41.9 1.0

Potassium binding site 4 out of 6 in 8ar7

Go back to Potassium Binding Sites List in 8ar7
Potassium binding site 4 out of 6 in the Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K603

b:69.3
occ:1.00
 O D:HOH710 2.4 70.9 1.0
O D:PRO114 2.5 52.2 1.0
O D:HIS142 2.7 45.6 1.0
OD1 D:ASN116 2.7 56.9 1.0
O D:ILE111 3.1 55.4 1.0
O D:ILE112 3.1 52.4 1.0
CG D:ASN116 3.4 55.6 1.0
C D:PRO114 3.7 52.0 1.0
C D:ILE112 3.7 52.4 1.0
ND2 D:ASN116 3.8 55.8 1.0
C D:HIS142 3.9 45.4 1.0
CA D:ILE112 4.0 53.0 1.0
N D:ASN116 4.0 51.9 1.0
NE2 D:HIS142 4.0 49.9 1.0
C D:ILE111 4.1 54.9 1.0
CD2 D:HIS142 4.2 48.8 1.0
CE1 D:HIS142 4.3 50.0 1.0
CA D:SER143 4.3 45.2 1.0
CB D:SER143 4.4 46.5 1.0
CB D:ASN116 4.4 53.0 1.0
N D:PRO114 4.4 51.5 1.0
C D:CYS115 4.5 52.3 1.0
N D:ILE112 4.5 53.5 1.0
N D:SER143 4.5 44.9 1.0
CA D:CYS115 4.5 52.4 1.0
N D:CYS115 4.6 52.0 1.0
OH D:TYR553 4.6 64.7 1.0
CG D:HIS142 4.6 47.7 1.0
CA D:ASN116 4.6 51.9 1.0
ND1 D:HIS142 4.6 49.3 1.0
CD D:PRO114 4.6 50.9 1.0
CA D:PRO114 4.7 51.6 1.0
N D:LYS113 4.8 51.8 1.0
C D:LYS113 4.8 51.6 1.0
OG D:SER143 4.8 48.4 1.0
CG D:PRO114 4.9 52.5 1.0
CA D:HIS142 4.9 45.4 1.0

Potassium binding site 5 out of 6 in 8ar7

Go back to Potassium Binding Sites List in 8ar7
Potassium binding site 5 out of 6 in the Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K603

b:52.7
occ:1.00
 O E:PRO114 2.6 46.0 1.0
O E:HOH718 2.6 36.8 1.0
OD1 E:ASN116 2.7 51.1 1.0
O E:HIS142 2.9 41.7 1.0
O E:ILE112 2.9 46.3 1.0
O E:ILE111 3.0 47.8 1.0
CG E:ASN116 3.4 50.0 1.0
C E:ILE112 3.7 46.0 1.0
ND2 E:ASN116 3.8 50.8 1.0
CA E:ILE112 3.8 46.4 1.0
C E:PRO114 3.9 45.6 1.0
C E:ILE111 3.9 47.4 1.0
C E:HIS142 4.0 41.3 1.0
N E:ASN116 4.1 44.6 1.0
NE2 E:HIS142 4.3 44.6 1.0
CE1 E:HIS142 4.3 44.9 1.0
N E:ILE112 4.3 46.7 1.0
CA E:SER143 4.5 40.3 1.0
CD2 E:HIS142 4.5 43.5 1.0
CB E:ASN116 4.5 46.2 1.0
OH E:TYR553 4.5 53.6 1.0
C E:CYS115 4.5 45.1 1.0
CB E:SER143 4.6 41.3 1.0
ND1 E:HIS142 4.6 44.3 1.0
N E:PRO114 4.6 45.5 1.0
CA E:CYS115 4.6 45.6 1.0
CA E:ASN116 4.6 44.7 1.0
CG E:HIS142 4.7 42.7 1.0
N E:CYS115 4.7 45.4 1.0
N E:SER143 4.7 40.5 1.0
N E:LYS113 4.8 45.3 1.0
CA E:PRO114 4.8 45.4 1.0
CD E:PRO114 4.8 45.2 1.0
C E:LYS113 4.9 45.7 1.0
OG E:SER143 4.9 43.3 1.0
CG E:PRO114 4.9 46.5 1.0
CG2 E:ILE111 4.9 48.2 1.0

Potassium binding site 6 out of 6 in 8ar7

Go back to Potassium Binding Sites List in 8ar7
Potassium binding site 6 out of 6 in the Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Bovine Glutamate Dehydrogenase in Ternary Complex with the Allosteric Activators Adp and Leucine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K602

b:56.0
occ:1.00
 OD1 F:ASN116 2.8 52.8 1.0
O F:ILE111 2.9 51.3 1.0
O F:PRO114 2.9 49.3 1.0
O F:HIS142 2.9 42.5 1.0
O F:ILE112 3.0 49.3 1.0
CG F:ASN116 3.5 51.2 1.0
C F:ILE112 3.7 49.1 1.0
CA F:ILE112 3.8 49.4 1.0
ND2 F:ASN116 3.9 52.0 1.0
C F:ILE111 3.9 51.3 1.0
C F:HIS142 4.0 42.2 1.0
CB F:SER143 4.0 43.7 1.0
O C:HOH714 4.1 46.1 1.0
CA F:SER143 4.1 42.2 1.0
OH F:TYR553 4.1 59.5 1.0
C F:PRO114 4.1 48.8 1.0
OG F:SER143 4.2 45.8 1.0
CE1 F:HIS142 4.3 47.4 1.0
N F:ILE112 4.3 50.1 1.0
NE2 F:HIS142 4.3 47.5 1.0
N F:ASN116 4.4 46.5 1.0
N F:SER143 4.5 42.0 1.0
ND1 F:HIS142 4.5 46.7 1.0
CD2 F:HIS142 4.6 46.2 1.0
CB F:ASN116 4.6 47.5 1.0
CG F:HIS142 4.8 45.0 1.0
N F:PRO114 4.8 48.8 1.0
N F:LYS113 4.9 48.5 1.0
CA F:ASN116 4.9 46.6 1.0
C F:CYS115 4.9 46.9 1.0
CG2 F:ILE111 5.0 53.7 1.0
CA F:CYS115 5.0 47.7 1.0
CD F:PRO114 5.0 48.3 1.0

Reference:

V.A.Aleshin, V.I.Bunik, E.M.Bruch, M.Bellinzoni. Structural Basis For the Binding of Allosteric Activators Leucine and Adp to Mammalian Glutamate Dehydrogenase. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36232607
DOI: 10.3390/IJMS231911306
Page generated: Wed Apr 5 10:34:58 2023

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