Sodium in PDB 1q7g: Homoserine Dehydrogenase in Complex with Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline

All present enzymatic activity of Homoserine Dehydrogenase in Complex with Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline:
1.1.1.3;

The structure of Homoserine Dehydrogenase in Complex with Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline, PDB code: 1q7g was solved by S.L.Jacques, I.A.Mirza, L.Ejim, K.Koteva, D.W.Hughes, K.Green, R.Kinach, J.F.Honek, H.K.Lai, A.M.Berghuis, G.D.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.43 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.863, 80.863, 248.986, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 30.6

The binding sites of Sodium atom in the Homoserine Dehydrogenase in Complex with Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline (pdb code 1q7g). 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 in Complex with Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline, PDB code: 1q7g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homoserine Dehydrogenase in Complex with Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homoserine Dehydrogenase in Complex with Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline within 5.0Å range: probe atom residue distance (Å) B Occ A:Na500 b:25.1 occ:1.00 O A:LEU150 2.7 21.2 1.0 OE2 A:GLU143 2.7 21.6 1.0 O A:VAL146 2.7 20.3 1.0 O A:GLU143 2.8 23.2 1.0 O A:ALA148 3.1 29.8 1.0 O A:GLY147 3.3 28.6 1.0 N A:LEU150 3.3 26.6 1.0 C A:GLY147 3.4 28.8 1.0 C A:LEU150 3.6 23.1 1.0 CD A:GLU143 3.7 22.4 1.0 C A:VAL146 3.7 22.3 1.0 C A:ALA148 3.7 28.6 1.0 CA A:GLY147 3.8 26.4 1.0 CG A:GLU143 3.9 20.9 1.0 CA A:LEU150 3.9 23.8 1.0 CG2 A:ILE152 3.9 18.8 1.0 C A:GLU143 4.0 22.3 1.0 N A:ALA148 4.0 28.6 1.0 C A:GLY149 4.1 28.1 1.0 CB A:LEU150 4.2 23.0 1.0 N A:GLY147 4.2 24.3 1.0 N A:GLY149 4.2 28.3 1.0 CA A:GLY149 4.3 28.4 1.0 CG1 A:ILE152 4.5 22.0 1.0 N A:ILE152 4.5 23.6 1.0 CA A:ALA148 4.5 28.5 1.0 CB A:ILE152 4.7 20.2 1.0 CA A:GLU143 4.7 21.7 1.0 OE1 A:GLU143 4.8 23.7 1.0 N A:PRO151 4.9 23.4 1.0 CB A:GLU143 4.9 22.1 1.0 CA A:VAL146 4.9 21.8 1.0 N A:ALA144 4.9 21.4 1.0 CA A:ALA144 4.9 21.7 1.0 CD1 A:ILE152 4.9 26.3 1.0 N A:VAL146 4.9 21.5 1.0 N A:ILE153 5.0 16.9 1.0

Sodium binding site 2 out of 2 in the Homoserine Dehydrogenase in Complex with Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homoserine Dehydrogenase in Complex with Suicide Inhibitor Complex Nad-5-Hydroxy-4-Oxonorvaline within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:34.3 occ:1.00 O B:GLU143 2.8 21.0 1.0 O B:LEU150 2.9 18.4 1.0 OE2 B:GLU143 3.0 27.5 1.0 O B:VAL146 3.0 21.5 1.0 O B:ALA148 3.1 21.2 1.0 O B:GLY147 3.3 19.2 1.0 CG B:GLU143 3.4 24.8 1.0 C B:GLU143 3.5 22.6 1.0 C B:GLY147 3.5 20.4 1.0 C B:ALA148 3.6 20.0 1.0 CD B:GLU143 3.6 26.6 1.0 N B:LEU150 3.7 19.6 1.0 C B:VAL146 3.7 19.1 1.0 C B:LEU150 4.0 19.8 1.0 N B:ALA148 4.0 19.7 1.0 CA B:GLY147 4.0 20.0 1.0 C B:GLY149 4.1 20.5 1.0 N B:GLY149 4.1 20.0 1.0 CA B:GLY149 4.2 20.1 1.0 N B:GLY147 4.2 20.1 1.0 CA B:GLU143 4.2 22.8 1.0 N B:ALA144 4.3 22.7 1.0 CB B:GLU143 4.3 22.9 1.0 CA B:LEU150 4.3 20.1 1.0 CA B:ALA148 4.4 20.4 1.0 CA B:ALA144 4.5 22.9 1.0 CB B:ILE152 4.5 22.1 1.0 N B:VAL146 4.5 18.6 1.0 CB B:LEU150 4.6 19.6 1.0 N B:ILE152 4.6 19.8 1.0 CA B:VAL146 4.7 18.7 1.0 CD1 B:ILE152 4.8 27.3 1.0 OE1 B:GLU143 4.8 27.1 1.0 O B:GLY149 4.9 20.6 1.0 C B:ALA144 4.9 23.5 1.0

S.L.Jacques, I.A.Mirza, L.Ejim, K.Koteva, D.W.Hughes, K.Green, R.Kinach, J.F.Honek, H.K.Lai, A.M.Berghuis, G.D.Wright. Enzyme Assisted Suicide: Molecular Basis For the Antifungal Activity of 5-Hydroxy-4-Oxonorvaline By Potent Inhibition of Homoserine Dehydrogenase Chem.Biol. V. 10 989 2003.
ISSN: ISSN 1074-5521
PubMed: 14583265
DOI: 10.1016/J.CHEMBIOL.2003.09.015