Magnesium in PDB 3ivs: Homocitrate Synthase LYS4

All present enzymatic activity of Homocitrate Synthase LYS4:
2.3.3.14;

The structure of Homocitrate Synthase LYS4, PDB code: 3ivs 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)	29.45 / 2.24
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	135.995, 135.995, 122.124, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 22

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

Cobalt

(Co)

2 atoms

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

Magnesium binding site 1 out of 2 in the Homocitrate Synthase LYS4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Homocitrate Synthase LYS4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:63.9 occ:1.00 O A:HOH520 2.0 54.1 1.0 O A:HOH506 2.1 52.1 1.0 O A:HOH517 2.1 56.4 1.0 O A:HOH497 2.1 46.9 1.0 OE2 A:GLU222 2.2 53.8 1.0 O A:HOH496 2.3 59.3 1.0 CD A:GLU222 3.3 52.9 1.0 O A:HOH509 3.5 50.9 1.0 OD2 A:ASP248 3.7 51.3 1.0 OD1 A:ASP248 3.8 50.3 1.0 OE1 A:GLU74 3.8 56.5 1.0 OD2 A:ASP123 3.8 56.4 1.0 CG A:GLU222 3.9 52.5 1.0 NH1 A:ARG163 4.0 55.8 1.0 O A:HOH494 4.1 60.6 1.0 CG A:ASP248 4.2 49.5 1.0 O A:HOH524 4.2 92.4 1.0 NH1 A:ARG43 4.2 59.9 1.0 OE2 A:GLU74 4.3 56.5 1.0 OE1 A:GLU222 4.4 54.6 1.0 CD A:GLU74 4.5 55.6 1.0 CB A:GLU222 4.6 51.2 1.0 O A:HOH532 4.7 53.2 1.0 CG A:ASP123 4.7 55.7 1.0 OG A:SER165 4.7 55.0 1.0 CD1 A:ILE38 4.7 48.1 1.0

Magnesium binding site 2 out of 2 in the Homocitrate Synthase LYS4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Homocitrate Synthase LYS4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:62.9 occ:1.00 O B:HOH513 2.0 54.8 1.0 O B:HOH524 2.0 55.8 1.0 O B:HOH503 2.1 46.0 1.0 OE2 B:GLU222 2.1 52.9 1.0 O B:HOH523 2.1 48.5 1.0 O B:HOH496 2.2 53.7 1.0 CD B:GLU222 3.2 53.2 1.0 O B:HOH463 3.6 50.5 1.0 OD2 B:ASP123 3.7 56.2 1.0 CG B:GLU222 3.8 54.4 1.0 NH1 B:ARG163 3.8 53.3 1.0 OD1 B:ASP248 3.8 49.5 1.0 OD2 B:ASP248 3.8 50.6 1.0 OE1 B:GLU74 3.9 54.0 1.0 O B:HOH536 4.2 94.3 1.0 CG B:ASP248 4.3 49.8 1.0 OE1 B:GLU222 4.3 55.0 1.0 NH1 B:ARG43 4.3 58.4 1.0 OE2 B:GLU74 4.4 55.0 1.0 CB B:GLU222 4.5 51.6 1.0 OG B:SER165 4.5 54.8 1.0 CD B:GLU74 4.6 54.2 1.0 CG B:ASP123 4.6 55.7 1.0 CD1 B:ILE38 4.7 49.1 1.0 O B:HOH499 4.8 53.3 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