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Sodium in PDB 8zmu: Glutamate Dehydrogenase (W89F-Mutant) From Thermococcus Profundus in the Unliganded State

Enzymatic activity of Glutamate Dehydrogenase (W89F-Mutant) From Thermococcus Profundus in the Unliganded State

All present enzymatic activity of Glutamate Dehydrogenase (W89F-Mutant) From Thermococcus Profundus in the Unliganded State:
1.4.1.3;

Protein crystallography data

The structure of Glutamate Dehydrogenase (W89F-Mutant) From Thermococcus Profundus in the Unliganded State, PDB code: 8zmu was solved by T.Wakabayashi, Y.Matsui, M.Masayoshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.80 / 2.03
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.355, 163.248, 132.605, 90, 113.91, 90
R / Rfree (%) 17.2 / 19.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Glutamate Dehydrogenase (W89F-Mutant) From Thermococcus Profundus in the Unliganded State (pdb code 8zmu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Glutamate Dehydrogenase (W89F-Mutant) From Thermococcus Profundus in the Unliganded State, PDB code: 8zmu:

Sodium binding site 1 out of 1 in 8zmu

Go back to Sodium Binding Sites List in 8zmu
Sodium binding site 1 out of 1 in the Glutamate Dehydrogenase (W89F-Mutant) From Thermococcus Profundus in the Unliganded State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glutamate Dehydrogenase (W89F-Mutant) From Thermococcus Profundus in the Unliganded State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na512

b:39.6
occ:1.00
 O4 B:SO4504 2.5 82.3 1.0
O B:HOH731 2.9 43.8 1.0
N B:ALA192 3.1 25.5 1.0
O B:GLY188 3.3 39.6 1.0
C B:THR189 3.4 23.5 1.0
N B:THR191 3.4 24.9 1.0
ND2 B:ASN222 3.5 45.4 1.0
O B:THR189 3.5 25.1 1.0
CA B:THR189 3.6 27.7 1.0
CB B:THR191 3.7 31.2 1.0
N B:ALA190 3.7 25.6 1.0
CB B:ALA192 3.8 28.2 1.0
CA B:THR191 3.8 26.6 1.0
S B:SO4504 3.8 77.2 1.0
C B:THR191 3.9 26.4 1.0
CA B:ALA192 4.1 25.8 1.0
C B:GLY188 4.1 32.9 1.0
C B:ALA190 4.3 24.3 1.0
N B:THR189 4.3 29.8 1.0
CA B:ALA223 4.3 28.1 1.0
O3 B:SO4504 4.4 85.0 1.0
O1 B:SO4504 4.4 95.1 1.0
O B:HOH609 4.4 49.4 1.0
OG1 B:THR191 4.6 33.8 1.0
CG2 B:THR191 4.6 31.4 1.0
CA B:ALA190 4.6 24.6 1.0
CB B:TYR226 4.6 29.2 1.0
CG B:ASN222 4.7 48.9 1.0
N B:ALA223 4.7 28.7 1.0
O B:ASN222 4.7 27.9 1.0
CB B:ALA223 4.8 33.2 1.0
O2 B:SO4504 4.8 85.9 1.0
CD2 B:TYR226 4.8 28.6 1.0
C B:ASN222 4.8 29.2 1.0
CB B:THR189 4.9 35.1 1.0

Reference:

T.Wakabayashi, Y.Matsui, M.Nakasako. Mechanism For Drastic Reduction in Catalytic Activity of TRP89PHE-Mutated Glutamate Dehydrogenase Revealed By Cryoem-Sampling Metastable Conformation in Action To Be Published.
Page generated: Mon Aug 18 16:31:55 2025

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