Sodium in PDB 6a0r: Homoserine Dehydrogenase From Thermus Thermophilus HB8 Unliganded Form

All present enzymatic activity of Homoserine Dehydrogenase From Thermus Thermophilus HB8 Unliganded Form:
1.1.1.3;

The structure of Homoserine Dehydrogenase From Thermus Thermophilus HB8 Unliganded Form, PDB code: 6a0r was solved by S.Akai, H.Ikushiro, T.Sawai, T.Yano, N.Kamiya, I.Miyahara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.83
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.197, 119.197, 144.547, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 17.7

The binding sites of Sodium atom in the Homoserine Dehydrogenase From Thermus Thermophilus HB8 Unliganded Form (pdb code 6a0r). 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 Unliganded Form, PDB code: 6a0r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8 Unliganded Form


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 Unliganded Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:15.2 occ:1.00 O B:VAL124 2.3 15.2 1.0 OE2 B:GLU121 2.3 15.6 1.0 O B:ALA126 2.3 14.2 1.0 O B:THR128 2.4 14.6 1.0 O B:GLU121 2.4 16.3 1.0 CD B:GLU121 3.3 14.7 1.0 C B:ALA126 3.4 15.8 1.0 C B:GLU121 3.5 17.1 1.0 CG B:GLU121 3.5 15.1 1.0 C B:VAL124 3.5 15.5 1.0 C B:THR128 3.6 15.6 1.0 C B:MET125 3.7 16.5 1.0 O B:MET125 3.8 14.8 1.0 CB B:ALA130 3.9 16.7 1.0 N B:ALA126 4.0 14.4 1.0 N B:ALA130 4.0 14.7 1.0 N B:THR128 4.0 16.0 1.0 CA B:GLU121 4.2 15.1 1.0 C B:GLY127 4.3 15.3 1.0 CA B:MET125 4.3 16.4 1.0 N B:MET125 4.3 15.1 1.0 CA B:ALA126 4.3 15.1 1.0 N B:GLY127 4.3 14.7 1.0 CB B:MET125 4.3 16.5 1.0 CA B:THR128 4.4 16.6 1.0 N B:ALA122 4.4 15.3 1.0 N B:VAL124 4.4 13.2 1.0 CA B:GLY127 4.4 15.8 1.0 CB B:GLU121 4.4 14.4 1.0 CA B:VAL124 4.4 15.4 1.0 C B:PRO129 4.4 17.0 1.0 CA B:ALA122 4.5 15.0 1.0 OE1 B:GLU121 4.5 16.2 1.0 CA B:ALA130 4.5 15.9 1.0 CA B:PRO129 4.5 14.9 1.0 N B:PRO129 4.5 13.2 1.0 N B:LEU131 4.8 14.1 1.0 C B:ALA122 4.8 13.7 1.0 CB B:VAL124 4.9 17.6 1.0 O B:GLY127 5.0 16.1 1.0

Sodium binding site 2 out of 2 in the Homoserine Dehydrogenase From Thermus Thermophilus HB8 Unliganded Form


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 Unliganded Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:14.7 occ:1.00 O A:VAL124 2.3 14.5 1.0 O A:ALA126 2.4 13.9 1.0 OE2 A:GLU121 2.4 14.8 1.0 O A:THR128 2.4 15.1 1.0 O A:GLU121 2.5 14.7 1.0 CD A:GLU121 3.3 15.9 1.0 C A:GLU121 3.5 14.1 1.0 C A:ALA126 3.5 15.2 1.0 C A:VAL124 3.5 16.1 1.0 CG A:GLU121 3.5 15.3 1.0 C A:THR128 3.6 15.2 1.0 C A:MET125 3.7 16.6 1.0 O A:MET125 3.8 14.4 1.0 CB A:ALA130 3.8 16.1 1.0 N A:ALA130 4.0 16.4 1.0 N A:ALA126 4.0 13.6 1.0 N A:THR128 4.0 14.2 1.0 CA A:GLU121 4.3 14.4 1.0 C A:GLY127 4.3 15.5 1.0 CA A:ALA126 4.3 14.8 1.0 N A:MET125 4.3 15.1 1.0 CA A:MET125 4.3 16.4 1.0 N A:ALA122 4.3 13.8 1.0 N A:GLY127 4.4 13.3 1.0 N A:VAL124 4.4 13.5 1.0 CB A:MET125 4.4 15.5 1.0 CA A:GLY127 4.4 14.1 1.0 CA A:THR128 4.4 16.0 1.0 CA A:ALA122 4.4 15.2 1.0 CA A:VAL124 4.4 15.2 1.0 C A:PRO129 4.5 16.8 1.0 CA A:ALA130 4.5 15.3 1.0 CB A:GLU121 4.5 14.8 1.0 OE1 A:GLU121 4.5 17.7 1.0 CA A:PRO129 4.5 16.3 1.0 N A:PRO129 4.5 13.8 1.0 N A:LEU131 4.7 15.7 1.0 C A:ALA122 4.9 14.8 1.0 CB A:VAL124 4.9 15.5 1.0 O A:GLY127 5.0 15.7 1.0

S.Akai, H.Ikushiro, T.Sawai, T.Yano, N.Kamiya, I.Miyahara. The Crystal Structure of Homoserine Dehydrogenase Complexed with L-Homoserine and Nadph in A Closed Form J. Biochem. V. 165 185 2019.
ISSN: ISSN 1756-2651
PubMed: 30423116
DOI: 10.1093/JB/MVY094