Sodium in PDB 3ivu: Homocitrate Synthase LYS4 Bound to 2-Og

All present enzymatic activity of Homocitrate Synthase LYS4 Bound to 2-Og:
2.3.3.14;

The structure of Homocitrate Synthase LYS4 Bound to 2-Og, PDB code: 3ivu was solved by S.L.Bulfer, E.M.Scott, J.-F.Couture, L.Pillus, R.C.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.41 / 2.72
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	133.798, 133.798, 125.657, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 21.7

The structure of Homocitrate Synthase LYS4 Bound to 2-Og also contains other interesting chemical elements:

Cobalt

(Co)

2 atoms

The binding sites of Sodium atom in the Homocitrate Synthase LYS4 Bound to 2-Og (pdb code 3ivu). 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 2-Og, PDB code: 3ivu:
Jump to Sodium binding site number: 1; 2;

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


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 2-Og within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:38.8 occ:0.50 O A:ARG214 2.9 55.0 1.0 O A:VAL217 3.1 54.2 1.0 O A:GLY215 3.4 56.1 1.0 C A:GLY215 3.7 55.0 1.0 CA A:GLY215 3.8 54.4 1.0 C A:ARG214 4.0 55.0 1.0 C A:VAL217 4.1 54.1 1.0 N A:GLY215 4.3 54.5 1.0 N A:VAL216 4.4 54.8 1.0 N A:VAL217 4.6 53.9 1.0 NE A:ARG214 4.6 55.4 1.0 CA A:SER218 4.7 55.1 1.0 NH2 A:ARG214 4.7 50.1 1.0 C A:VAL216 4.8 54.1 1.0 N A:SER218 4.8 54.6 1.0 CA A:VAL217 5.0 53.6 1.0

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


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 2-Og within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:37.3 occ:0.50 O B:ARG214 2.8 53.0 1.0 O B:VAL217 2.9 52.4 1.0 O B:GLY215 3.5 54.3 1.0 C B:GLY215 3.8 53.2 1.0 C B:VAL217 3.9 52.1 1.0 CA B:GLY215 4.0 53.1 1.0 C B:ARG214 4.0 53.3 1.0 N B:GLY215 4.5 52.9 1.0 CA B:SER218 4.5 53.5 1.0 N B:VAL217 4.5 51.9 1.0 N B:SER218 4.6 52.8 1.0 N B:VAL216 4.6 53.0 1.0 NH2 B:ARG214 4.6 47.3 1.0 NE B:ARG214 4.7 52.1 1.0 C B:VAL216 4.8 52.2 1.0 CA B:VAL217 4.8 51.5 1.0 CB B:SER218 4.9 53.5 1.0

S.L.Bulfer, E.M.Scott, J.F.Couture, L.Pillus, R.C.Trievel. Crystal Structure and Functional Analysis of Homocitrate Synthase, An Essential Enzyme in Lysine Biosynthesis. J.Biol.Chem. V. 284 35769 2009.
ISSN: ISSN 0021-9258
PubMed: 19776021
DOI: 10.1074/JBC.M109.046821