Magnesium in PDB 5iys: Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand

The structure of Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand, PDB code: 5iys was solved by G.Z.Liu, W.D.Liu, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.238, 41.090, 93.477, 90.00, 96.35, 90.00
R / Rfree (%)	16.4 / 22

The binding sites of Magnesium atom in the Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand (pdb code 5iys). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand, PDB code: 5iys:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:46.2 occ:1.00 O A:HOH607 1.7 31.3 1.0 O A:HOH642 1.8 31.8 1.0 O2A A:FPS507 1.9 40.7 1.0 O A:HOH614 2.0 33.8 1.0 OD1 A:ASN169 2.1 22.8 1.0 PA A:FPS507 3.2 46.3 1.0 CG A:ASN169 3.3 23.7 1.0 O3A A:FPS507 3.4 47.5 1.0 OD2 A:ASP173 3.7 28.0 1.0 ND2 A:ASN169 4.0 28.0 1.0 OD2 A:ASP177 4.0 33.8 1.0 S1 A:FPS507 4.0 52.2 1.0 OD1 A:ASP177 4.2 27.8 1.0 O A:ASN169 4.3 16.5 1.0 O1A A:FPS507 4.3 45.1 1.0 O A:HOH662 4.4 34.1 1.0 CB A:ASN169 4.5 18.7 1.0 C A:ASN169 4.5 21.4 1.0 CG A:ASP177 4.5 30.7 1.0 CG A:ASP173 4.6 25.1 1.0 CB A:ASP173 4.6 25.0 1.0 OE1 A:GLN166 4.6 40.4 1.0 PB A:FPS507 4.8 53.7 1.0 O1B A:FPS507 4.9 55.3 1.0 N A:ILE170 4.9 17.2 1.0 CE2 A:TYR184 4.9 32.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:37.1 occ:1.00 OD2 A:ASP60 2.0 43.8 1.0 OD1 A:ASP56 2.1 24.9 1.0 O A:HOH627 2.2 39.8 1.0 O A:HOH734 2.3 33.6 1.0 O1A A:FPS507 2.3 45.1 1.0 O A:HOH662 2.3 34.1 1.0 CG A:ASP60 3.0 45.9 1.0 CG A:ASP56 3.2 30.9 1.0 MG A:MG505 3.3 43.6 1.0 OD1 A:ASP60 3.4 39.0 1.0 PA A:FPS507 3.6 46.3 1.0 OD2 A:ASP56 3.7 37.9 1.0 O2A A:FPS507 3.9 40.7 1.0 OE1 A:GLN113 4.1 30.0 1.0 OD2 A:ASP116 4.1 46.6 1.0 NE2 A:GLN113 4.2 24.5 1.0 CB A:ASP60 4.3 43.9 1.0 C2 A:FPS507 4.3 39.6 1.0 S1 A:FPS507 4.4 52.2 1.0 CB A:ASP56 4.5 27.8 1.0 NH1 A:ARG182 4.6 49.3 1.0 CD A:GLN113 4.6 27.5 1.0 O A:HOH653 4.6 43.6 1.0 C3 A:FPS507 4.8 38.6 1.0 O A:ASP56 4.8 33.0 1.0 C1 A:FPS507 4.9 43.9 1.0 C5 A:FPS507 4.9 33.5 1.0 O A:HOH619 4.9 36.2 1.0 OH A:TYR131 5.0 28.9 1.0 O2B A:FPS507 5.0 53.7 1.0 O3A A:FPS507 5.0 47.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:43.6 occ:1.00 O A:HOH619 2.1 36.2 1.0 OD2 A:ASP56 2.2 37.9 1.0 O1A A:FPS507 2.2 45.1 1.0 O2B A:FPS507 2.3 53.7 1.0 O A:HOH653 2.3 43.6 1.0 OD2 A:ASP60 2.5 43.8 1.0 CG A:ASP56 3.1 30.9 1.0 OD1 A:ASP56 3.2 24.9 1.0 MG A:MG504 3.3 37.1 1.0 CG A:ASP60 3.3 45.9 1.0 PB A:FPS507 3.4 53.7 1.0 PA A:FPS507 3.4 46.3 1.0 CB A:ASP60 3.4 43.9 1.0 O3A A:FPS507 3.7 47.5 1.0 O1B A:FPS507 3.8 55.3 1.0 O A:HOH603 4.0 47.6 1.0 NH1 A:ARG53 4.0 31.5 1.0 O2A A:FPS507 4.3 40.7 1.0 O A:ASP56 4.4 33.0 1.0 O A:HOH662 4.4 34.1 1.0 CB A:ASP56 4.5 27.8 1.0 OD1 A:ASP60 4.5 39.0 1.0 O3B A:FPS507 4.6 49.1 1.0 C2 A:FPS507 4.7 39.6 1.0 C1 A:FPS507 4.7 43.9 1.0 C A:ASP56 4.9 31.3 1.0 CA A:ASP60 4.9 45.9 1.0 S1 A:FPS507 4.9 52.2 1.0 O A:HOH627 5.0 39.8 1.0

G.Z.Liu, W.D.Liu, C.C.Chen, R.T.Guo. Crystal Structure of A Dehydrosqualene Synthase in Complex with Ligand To Be Published.