Cobalt 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:

Sodium

(Na)

2 atoms

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

Cobalt 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 Cobalt with other atoms in the Co binding site number 1 of Homocitrate Synthase LYS4 Bound to 2-Og within 5.0Å range: probe atom residue distance (Å) B Occ A:Co500 b:63.8 occ:1.00 OE1 A:GLU44 2.0 59.5 1.0 O1 A:AKG1000 2.0 69.6 1.0 O A:HOH465 2.0 62.6 1.0 O5 A:AKG1000 2.0 72.6 1.0 NE2 A:HIS226 2.1 62.3 1.0 NE2 A:HIS224 2.1 60.1 1.0 C1 A:AKG1000 2.7 73.0 1.0 C2 A:AKG1000 2.7 74.6 1.0 CD2 A:HIS226 2.9 60.0 1.0 CE1 A:HIS224 3.0 58.1 1.0 CD A:GLU44 3.0 60.8 1.0 CD2 A:HIS224 3.2 58.2 1.0 CE1 A:HIS226 3.2 59.9 1.0 OE2 A:GLU44 3.4 61.1 1.0 O2 A:AKG1000 3.9 71.5 1.0 CG2 A:ILE260 4.1 56.7 1.0 C3 A:AKG1000 4.1 77.4 1.0 ND1 A:HIS224 4.1 58.0 1.0 CG A:HIS226 4.1 60.5 1.0 O A:HOH451 4.1 49.1 1.0 ND1 A:HIS226 4.2 58.3 1.0 NH2 A:ARG43 4.2 74.5 1.0 CG A:HIS224 4.2 57.3 1.0 CG A:GLU44 4.4 60.8 1.0 C4 A:AKG1000 4.5 82.2 1.0 CB A:GLU44 5.0 59.9 1.0

Cobalt 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 Cobalt with other atoms in the Co binding site number 2 of Homocitrate Synthase LYS4 Bound to 2-Og within 5.0Å range: probe atom residue distance (Å) B Occ B:Co500 b:64.4 occ:1.00 OE1 B:GLU44 2.0 60.5 1.0 O5 B:AKG1000 2.0 74.8 1.0 O B:HOH422 2.0 62.8 1.0 O1 B:AKG1000 2.0 72.2 1.0 NE2 B:HIS226 2.1 60.1 1.0 NE2 B:HIS224 2.1 58.4 1.0 C2 B:AKG1000 2.7 76.6 1.0 C1 B:AKG1000 2.7 75.4 1.0 CE1 B:HIS224 2.9 57.9 1.0 CD2 B:HIS226 3.0 57.5 1.0 CD B:GLU44 3.1 62.0 1.0 CE1 B:HIS226 3.1 57.2 1.0 CD2 B:HIS224 3.2 56.8 1.0 OE2 B:GLU44 3.6 60.6 1.0 O2 B:AKG1000 3.9 74.3 1.0 O B:HOH435 4.0 52.0 1.0 NH2 B:ARG43 4.1 72.6 1.0 ND1 B:HIS224 4.1 57.4 1.0 CG2 B:ILE260 4.1 55.7 1.0 CG B:HIS226 4.2 56.8 1.0 C3 B:AKG1000 4.2 79.4 1.0 ND1 B:HIS226 4.2 56.1 1.0 CG B:HIS224 4.3 56.9 1.0 CG B:GLU44 4.4 61.0 1.0 C4 B:AKG1000 4.6 83.3 1.0 CB B:GLU44 5.0 60.5 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