Sodium in PDB 6a0t: Homoserine Dehydrogenase K99A Mutant From Thermus Thermophilus HB8 Complexed with Hse and Nadp+

All present enzymatic activity of Homoserine Dehydrogenase K99A Mutant From Thermus Thermophilus HB8 Complexed with Hse and Nadp+:
1.1.1.3;

The structure of Homoserine Dehydrogenase K99A Mutant From Thermus Thermophilus HB8 Complexed with Hse and Nadp+, PDB code: 6a0t 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 / 1.87
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.401, 121.401, 145.089, 90.00, 90.00, 120.00
R / Rfree (%)	13.7 / 16.7

The binding sites of Sodium atom in the Homoserine Dehydrogenase K99A Mutant From Thermus Thermophilus HB8 Complexed with Hse and Nadp+ (pdb code 6a0t). 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 K99A Mutant From Thermus Thermophilus HB8 Complexed with Hse and Nadp+, PDB code: 6a0t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homoserine Dehydrogenase K99A Mutant From Thermus Thermophilus HB8 Complexed with Hse and Nadp+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homoserine Dehydrogenase K99A Mutant From Thermus Thermophilus HB8 Complexed with Hse and Nadp+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:12.5 occ:1.00 O B:VAL124 2.3 12.6 1.0 O B:ALA126 2.3 11.7 1.0 OE2 B:GLU121 2.4 12.8 1.0 O B:GLU121 2.4 12.3 1.0 O B:THR128 2.4 12.5 1.0 CD B:GLU121 3.3 13.2 1.0 C B:GLU121 3.4 12.1 1.0 C B:ALA126 3.4 13.9 1.0 C B:VAL124 3.5 12.3 1.0 CG B:GLU121 3.5 13.2 1.0 C B:THR128 3.6 12.6 1.0 O B:MET125 3.7 12.1 1.0 C B:MET125 3.7 12.8 1.0 N B:ALA126 3.9 12.7 1.0 N B:ALA130 3.9 15.3 1.0 N B:THR128 4.0 12.5 1.0 CB B:ALA130 4.1 16.8 1.0 CA B:GLU121 4.2 12.1 1.0 N B:MET125 4.2 11.6 1.0 CA B:MET125 4.3 12.7 1.0 CA B:ALA126 4.3 12.6 1.0 C B:GLY127 4.3 13.7 1.0 CB B:MET125 4.3 13.3 1.0 N B:ALA122 4.3 11.8 1.0 N B:GLY127 4.3 13.5 1.0 CB B:GLU121 4.4 12.0 1.0 N B:VAL124 4.4 11.8 1.0 CA B:ALA122 4.4 12.6 1.0 CA B:THR128 4.4 14.2 1.0 CA B:GLY127 4.4 13.1 1.0 CA B:VAL124 4.4 11.6 1.0 OE1 B:GLU121 4.5 15.5 1.0 CA B:PRO129 4.6 14.4 1.0 N B:PRO129 4.6 12.2 1.0 C B:PRO129 4.6 16.6 1.0 CA B:ALA130 4.6 14.4 1.0 C B:ALA122 4.8 12.6 1.0 N B:LEU131 4.8 12.8 1.0 CB B:VAL124 4.9 12.5 1.0 O B:GLY127 5.0 13.8 1.0

Sodium binding site 2 out of 2 in the Homoserine Dehydrogenase K99A Mutant From Thermus Thermophilus HB8 Complexed with Hse and Nadp+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homoserine Dehydrogenase K99A Mutant From Thermus Thermophilus HB8 Complexed with Hse and Nadp+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:12.3 occ:1.00 O A:VAL124 2.3 12.5 1.0 O A:ALA126 2.3 11.4 1.0 OE2 A:GLU121 2.3 12.8 1.0 O A:GLU121 2.4 12.0 1.0 O A:THR128 2.5 11.7 1.0 CD A:GLU121 3.2 12.5 1.0 C A:ALA126 3.4 11.7 1.0 C A:GLU121 3.4 10.4 1.0 CG A:GLU121 3.4 11.2 1.0 C A:VAL124 3.5 12.5 1.0 O A:MET125 3.6 11.8 1.0 C A:MET125 3.7 12.9 1.0 C A:THR128 3.7 13.0 1.0 N A:ALA126 3.8 11.7 1.0 N A:ALA130 3.9 16.9 1.0 N A:THR128 4.0 11.9 1.0 CB A:ALA130 4.1 17.1 1.0 CA A:GLU121 4.2 11.4 1.0 CA A:MET125 4.2 12.8 1.0 CA A:ALA126 4.2 11.3 1.0 N A:MET125 4.2 12.8 1.0 C A:GLY127 4.3 12.2 1.0 N A:ALA122 4.3 11.9 1.0 CB A:MET125 4.4 13.5 1.0 N A:GLY127 4.4 11.5 1.0 N A:VAL124 4.4 11.6 1.0 CA A:ALA122 4.4 12.2 1.0 CB A:GLU121 4.4 11.9 1.0 OE1 A:GLU121 4.4 13.2 1.0 CA A:VAL124 4.4 11.8 1.0 CA A:GLY127 4.4 11.6 1.0 CA A:THR128 4.4 12.2 1.0 CA A:ALA130 4.6 16.9 1.0 CA A:PRO129 4.6 14.6 1.0 N A:PRO129 4.6 12.3 1.0 C A:PRO129 4.7 18.4 1.0 C A:ALA122 4.8 12.4 1.0 N A:LEU131 4.8 13.8 1.0 CB A:VAL124 4.9 13.4 1.0 O A:GLY127 5.0 11.6 1.0 CB A:THR128 5.0 12.3 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