Zinc in PDB 3ivt: 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: 3ivt 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)	39.47 / 2.67
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	133.731, 133.731, 125.904, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 20.6

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

Sodium

(Na)

2 atoms

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

Zinc 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 Zinc with other atoms in the Zn binding site number 1 of Homocitrate Synthase LYS4 Bound to 2-Og within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:48.2 occ:1.00 OE1 A:GLU44 2.0 44.9 1.0 O5 A:AKG1000 2.0 58.9 1.0 O1 A:AKG1000 2.0 54.9 1.0 O A:HOH419 2.0 48.3 1.0 NE2 A:HIS226 2.1 45.8 1.0 NE2 A:HIS224 2.1 46.3 1.0 C2 A:AKG1000 2.7 59.1 1.0 C1 A:AKG1000 2.7 57.6 1.0 CD A:GLU44 3.0 51.3 1.0 CE1 A:HIS224 3.0 45.1 1.0 CD2 A:HIS226 3.0 44.8 1.0 CE1 A:HIS226 3.1 44.6 1.0 CD2 A:HIS224 3.1 45.1 1.0 OE2 A:GLU44 3.3 52.1 1.0 O A:HOH439 3.6 72.3 1.0 O2 A:AKG1000 4.0 55.9 1.0 CG2 A:ILE260 4.0 44.5 1.0 ND1 A:HIS224 4.1 46.4 1.0 CG A:HIS226 4.1 45.6 1.0 ND1 A:HIS226 4.2 44.5 1.0 C3 A:AKG1000 4.2 60.1 1.0 O A:HOH443 4.2 55.4 1.0 CG A:HIS224 4.2 46.0 1.0 NH2 A:ARG43 4.2 57.0 1.0 CG A:GLU44 4.3 51.8 1.0 C4 A:AKG1000 4.6 60.0 1.0 CB A:GLU44 4.9 50.9 1.0

Zinc 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 Zinc with other atoms in the Zn binding site number 2 of Homocitrate Synthase LYS4 Bound to 2-Og within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:47.8 occ:1.00 OE1 B:GLU44 2.0 45.1 1.0 O5 B:AKG1000 2.0 57.1 1.0 O B:HOH419 2.0 48.3 1.0 O1 B:AKG1000 2.0 53.5 1.0 NE2 B:HIS224 2.1 46.5 1.0 NE2 B:HIS226 2.1 47.4 1.0 C2 B:AKG1000 2.8 56.8 1.0 C1 B:AKG1000 2.8 55.9 1.0 CE1 B:HIS224 2.9 46.4 1.0 CD B:GLU44 3.0 50.6 1.0 CD2 B:HIS226 3.0 46.8 1.0 CE1 B:HIS226 3.1 47.8 1.0 CD2 B:HIS224 3.2 46.1 1.0 OE2 B:GLU44 3.4 49.2 1.0 O B:HOH473 3.9 72.5 1.0 O2 B:AKG1000 4.0 55.7 1.0 ND1 B:HIS224 4.1 47.6 1.0 CG2 B:ILE260 4.1 46.8 1.0 CG B:HIS226 4.1 47.6 1.0 NH2 B:ARG43 4.2 55.3 1.0 ND1 B:HIS226 4.2 46.4 1.0 C3 B:AKG1000 4.2 56.7 1.0 CG B:HIS224 4.2 46.4 1.0 O B:HOH443 4.3 47.6 1.0 CG B:GLU44 4.3 50.8 1.0 C4 B:AKG1000 4.6 56.6 1.0 CB B:GLU44 4.9 49.9 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