Sodium in PDB 5xdf: Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse

All present enzymatic activity of Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse:
1.1.1.3;

The structure of Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse, PDB code: 5xdf was solved by S.Akai, I.Miyahara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.625, 119.625, 145.020, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 21.9

The binding sites of Sodium atom in the Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse (pdb code 5xdf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse, PDB code: 5xdf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1302 b:23.0 occ:1.00 O A:ALA126 2.3 22.0 1.0 O A:VAL124 2.3 21.7 1.0 OE2 A:GLU121 2.4 18.7 1.0 O A:THR128 2.4 18.7 1.0 O A:GLU121 2.4 19.8 1.0 CD A:GLU121 3.3 23.8 1.0 C A:ALA126 3.4 23.9 1.0 C A:VAL124 3.4 22.2 1.0 C A:GLU121 3.5 21.2 1.0 CG A:GLU121 3.6 20.0 1.0 C A:THR128 3.6 21.5 1.0 O A:MET125 3.7 20.2 1.0 C A:MET125 3.7 22.0 1.0 N A:ALA126 3.9 19.4 1.0 CB A:ALA130 4.0 24.1 1.0 N A:ALA130 4.0 22.9 1.0 N A:THR128 4.0 23.3 1.0 CA A:GLU121 4.2 20.0 1.0 N A:MET125 4.3 18.8 1.0 CA A:ALA126 4.3 24.3 1.0 CA A:MET125 4.3 23.3 1.0 C A:GLY127 4.3 23.5 1.0 CB A:MET125 4.3 22.7 1.0 N A:GLY127 4.4 23.9 1.0 N A:ALA122 4.4 24.2 1.0 N A:VAL124 4.4 22.1 1.0 CA A:THR128 4.4 23.3 1.0 CA A:VAL124 4.4 21.7 1.0 CB A:GLU121 4.4 20.0 1.0 CA A:GLY127 4.5 23.0 1.0 C A:PRO129 4.5 24.7 1.0 OE1 A:GLU121 4.5 22.6 1.0 CA A:ALA122 4.5 23.0 1.0 N A:PRO129 4.5 22.4 1.0 CA A:PRO129 4.5 24.6 1.0 CA A:ALA130 4.6 24.3 1.0 N A:LEU131 4.8 20.9 1.0 C A:ALA122 4.8 24.2 1.0 CB A:VAL124 4.9 22.2 1.0

Sodium binding site 2 out of 2 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:20.4 occ:1.00 O B:VAL124 2.2 19.4 1.0 O B:ALA126 2.3 19.6 1.0 O B:GLU121 2.4 18.5 1.0 OE2 B:GLU121 2.4 20.7 1.0 O B:THR128 2.4 19.9 1.0 CD B:GLU121 3.3 22.2 1.0 C B:GLU121 3.5 21.5 1.0 C B:VAL124 3.5 20.6 1.0 C B:ALA126 3.5 23.5 1.0 CG B:GLU121 3.5 20.8 1.0 C B:THR128 3.6 22.4 1.0 O B:MET125 3.7 19.4 1.0 C B:MET125 3.8 23.1 1.0 N B:ALA130 3.9 22.6 1.0 CB B:ALA130 3.9 23.0 1.0 N B:ALA126 4.0 20.9 1.0 N B:THR128 4.0 21.7 1.0 CA B:GLU121 4.3 22.6 1.0 C B:GLY127 4.3 20.1 1.0 N B:MET125 4.3 18.5 1.0 CA B:ALA126 4.3 22.1 1.0 N B:ALA122 4.3 20.8 1.0 CA B:MET125 4.4 21.5 1.0 N B:GLY127 4.4 19.1 1.0 CA B:THR128 4.4 21.8 1.0 C B:PRO129 4.4 24.0 1.0 N B:VAL124 4.4 18.0 1.0 CB B:MET125 4.4 21.6 1.0 CA B:ALA122 4.4 23.5 1.0 CA B:VAL124 4.4 17.5 1.0 CB B:GLU121 4.5 21.3 1.0 CA B:GLY127 4.5 20.8 1.0 CA B:ALA130 4.5 22.0 1.0 OE1 B:GLU121 4.5 23.8 1.0 CA B:PRO129 4.5 22.1 1.0 N B:PRO129 4.6 20.4 1.0 N B:LEU131 4.8 20.4 1.0 C B:ALA122 4.9 21.0 1.0 CB B:VAL124 4.9 18.6 1.0 O B:GLY127 5.0 22.2 1.0

S.Akai, H.Ikushiro, D.Sawai, H.Hayashi, N.Kamiya, I.Miyahara. Crystallographic Study of Homoserine Dehydrogenase From Thermus Thermophilus HB8 To Be Published.