Sodium in PDB 6a0s: Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse and Nadph

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

The structure of Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse and Nadph, PDB code: 6a0s 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)	50.00 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.619, 119.619, 144.338, 90.00, 90.00, 120.00
R / Rfree (%)	15.9 / 20

The binding sites of Sodium atom in the Homoserine Dehydrogenase From Thermus Thermophilus HB8 Complexed with Hse and Nadph (pdb code 6a0s). 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 and Nadph, PDB code: 6a0s:
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 and Nadph


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 and Nadph within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:24.8 occ:1.00 O B:VAL124 2.3 23.9 1.0 O B:ALA126 2.3 23.1 1.0 OE2 B:GLU121 2.4 21.3 1.0 O B:THR128 2.4 24.5 1.0 O B:GLU121 2.4 23.3 1.0 CD B:GLU121 3.3 25.6 1.0 C B:ALA126 3.5 26.6 1.0 C B:VAL124 3.5 26.1 1.0 C B:GLU121 3.5 24.8 1.0 CG B:GLU121 3.5 23.1 1.0 C B:THR128 3.6 23.8 1.0 C B:MET125 3.7 25.4 1.0 O B:MET125 3.7 23.4 1.0 N B:ALA126 3.9 24.5 1.0 CB B:ALA130 3.9 30.3 1.0 N B:ALA130 4.0 25.9 1.0 N B:THR128 4.1 26.1 1.0 CA B:ALA126 4.3 26.2 1.0 CA B:GLU121 4.3 23.3 1.0 CA B:MET125 4.3 26.6 1.0 N B:MET125 4.3 22.5 1.0 CB B:MET125 4.3 25.9 1.0 C B:GLY127 4.3 26.3 1.0 N B:GLY127 4.3 24.5 1.0 CA B:GLY127 4.4 27.2 1.0 N B:ALA122 4.4 27.0 1.0 CA B:ALA122 4.4 25.0 1.0 N B:VAL124 4.4 24.9 1.0 CA B:VAL124 4.4 24.5 1.0 CA B:THR128 4.4 25.7 1.0 CB B:GLU121 4.5 23.2 1.0 OE1 B:GLU121 4.5 24.3 1.0 C B:PRO129 4.5 28.0 1.0 CA B:ALA130 4.5 29.3 1.0 N B:PRO129 4.5 23.7 1.0 CA B:PRO129 4.6 27.5 1.0 C B:ALA122 4.8 23.2 1.0 N B:LEU131 4.9 22.4 1.0 CB B:VAL124 4.9 27.4 1.0

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


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 and Nadph within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:23.6 occ:1.00 O A:VAL124 2.3 22.9 1.0 O A:ALA126 2.3 25.0 1.0 O A:GLU121 2.3 21.3 1.0 OE2 A:GLU121 2.4 23.4 1.0 O A:THR128 2.4 24.6 1.0 CD A:GLU121 3.3 23.5 1.0 C A:ALA126 3.4 26.6 1.0 C A:GLU121 3.4 22.3 1.0 CG A:GLU121 3.5 22.8 1.0 C A:VAL124 3.5 24.6 1.0 C A:THR128 3.6 24.5 1.0 C A:MET125 3.7 26.9 1.0 O A:MET125 3.7 24.4 1.0 CB A:ALA130 3.9 28.3 1.0 N A:ALA126 3.9 24.2 1.0 N A:ALA130 4.0 23.7 1.0 N A:THR128 4.0 24.7 1.0 CA A:GLU121 4.2 22.8 1.0 CA A:ALA126 4.2 24.9 1.0 CA A:MET125 4.3 25.5 1.0 C A:GLY127 4.3 24.1 1.0 N A:MET125 4.3 22.5 1.0 N A:GLY127 4.3 22.0 1.0 N A:ALA122 4.3 22.4 1.0 CB A:GLU121 4.4 23.0 1.0 CB A:MET125 4.4 26.1 1.0 CA A:GLY127 4.4 24.6 1.0 CA A:ALA122 4.4 24.3 1.0 N A:VAL124 4.4 21.4 1.0 CA A:THR128 4.5 25.4 1.0 CA A:ALA130 4.5 26.4 1.0 CA A:VAL124 4.5 20.9 1.0 C A:PRO129 4.5 26.2 1.0 OE1 A:GLU121 4.5 25.8 1.0 CA A:PRO129 4.6 24.5 1.0 N A:PRO129 4.6 25.0 1.0 N A:LEU131 4.8 25.8 1.0 C A:ALA122 4.8 23.6 1.0 CB A:VAL124 5.0 25.1 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