Sodium in PDB 3mi3: Homocitrate Synthase LYS4 Bound to Lysine

All present enzymatic activity of Homocitrate Synthase LYS4 Bound to Lysine:
2.3.3.14;

The structure of Homocitrate Synthase LYS4 Bound to Lysine, PDB code: 3mi3 was solved by S.L.Bulfer, E.M.Scott, L.Pillus, R.C.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.69 / 2.38
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	135.637, 135.637, 122.928, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 20.3

The structure of Homocitrate Synthase LYS4 Bound to Lysine also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Homocitrate Synthase LYS4 Bound to Lysine (pdb code 3mi3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Homocitrate Synthase LYS4 Bound to Lysine, PDB code: 3mi3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homocitrate Synthase LYS4 Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homocitrate Synthase LYS4 Bound to Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:28.4 occ:0.50 O A:HOH602 2.3 50.9 1.0 O A:VAL217 2.9 44.7 1.0 O A:ARG214 3.0 45.2 1.0 O A:GLY215 3.6 44.2 1.0 C A:VAL217 3.9 44.9 1.0 C A:GLY215 3.9 43.3 1.0 CA A:GLY215 4.1 42.9 1.0 C A:ARG214 4.1 44.5 1.0 CA A:SER218 4.5 46.8 1.0 N A:VAL217 4.5 44.9 1.0 NH2 A:ARG214 4.5 41.0 1.0 N A:SER218 4.6 45.9 1.0 N A:VAL216 4.6 44.5 1.0 N A:GLY215 4.6 43.7 1.0 C A:VAL216 4.7 44.4 1.0 NE A:ARG214 4.7 43.2 1.0 CA A:VAL217 4.8 44.2 1.0

Sodium binding site 2 out of 2 in the Homocitrate Synthase LYS4 Bound to Lysine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homocitrate Synthase LYS4 Bound to Lysine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:25.2 occ:0.50 O B:HOH737 2.5 53.2 1.0 O B:VAL217 2.9 46.6 1.0 O B:ARG214 2.9 45.7 1.0 O B:GLY215 3.3 47.1 1.0 C B:GLY215 3.8 45.3 1.0 C B:VAL217 3.8 46.4 1.0 CA B:GLY215 4.0 44.5 1.0 C B:ARG214 4.0 45.7 1.0 N B:VAL217 4.4 45.8 1.0 N B:GLY215 4.5 45.2 1.0 CA B:SER218 4.5 46.9 0.5 N B:VAL216 4.6 45.7 1.0 N B:SER218 4.6 46.5 1.0 NH2 B:ARG214 4.6 41.9 1.0 CA B:SER218 4.6 46.4 0.5 C B:VAL216 4.6 45.2 1.0 CA B:VAL217 4.7 45.8 1.0 OG B:SER218 4.7 48.2 0.5 NE B:ARG214 4.8 45.4 1.0 O B:VAL216 5.0 44.6 1.0

S.L.Bulfer, E.M.Scott, L.Pillus, R.C.Trievel. Structural Basis For L-Lysine Feedback Inhibition of Homocitrate Synthase J.Biol.Chem. V. 285 10446 2010.
ISSN: ISSN 0021-9258
PubMed: 20089861