Magnesium in PDB 4edz: Crystal Structure of Hh-Pgds with Water Displacing Inhibitor

All present enzymatic activity of Crystal Structure of Hh-Pgds with Water Displacing Inhibitor:
2.5.1.18; 5.3.99.2;

The structure of Crystal Structure of Hh-Pgds with Water Displacing Inhibitor, PDB code: 4edz was solved by J.E.Day, A.Thorarensen, J.I.Trujillo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	124.468, 124.468, 105.927, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.6

The binding sites of Magnesium atom in the Crystal Structure of Hh-Pgds with Water Displacing Inhibitor (pdb code 4edz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Hh-Pgds with Water Displacing Inhibitor, PDB code: 4edz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Hh-Pgds with Water Displacing Inhibitor


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 Hh-Pgds with Water Displacing Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:25.3 occ:1.00 O B:HOH302 2.0 13.0 1.0 O A:HOH301 2.1 16.9 1.0 O A:HOH302 2.1 15.0 1.0 O B:HOH301 2.1 17.1 1.0 OD2 B:ASP96 3.9 21.1 1.0 OD2 A:ASP96 3.9 20.0 1.0 OD2 B:ASP97 3.9 23.8 1.0 OD2 A:ASP97 4.0 19.8 1.0 O A:HOH303 4.1 18.5 1.0 O B:HOH312 4.1 15.8 1.0 OD2 B:ASP93 4.4 22.1 1.0 OD2 A:ASP93 4.4 20.1 1.0 CG B:ASP93 4.4 22.9 1.0 CG A:ASP93 4.5 21.1 1.0 OD1 B:ASP93 4.5 24.0 1.0 OD1 A:ASP93 4.5 21.9 1.0 CG B:ASP96 4.8 20.3 1.0 CG A:ASP96 4.9 18.9 1.0 CB B:ASP96 5.0 20.1 1.0 O B:HOH353 5.0 17.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Hh-Pgds with Water Displacing Inhibitor


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 Hh-Pgds with Water Displacing Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:12.4 occ:1.00 O D:HOH2502 1.9 11.4 1.0 O D:HOH2501 1.9 12.6 1.0 O C:HOH303 1.9 13.5 1.0 O C:HOH301 2.1 15.0 1.0 O C:HOH302 2.1 23.8 1.0 O D:HOH2503 2.1 17.3 1.0 OD2 D:ASP96 3.9 22.4 1.0 OD2 C:ASP96 4.0 19.5 1.0 OD2 C:ASP97 4.0 17.6 1.0 O D:HOH2504 4.0 15.4 1.0 O C:HOH308 4.1 21.7 1.0 O C:HOH381 4.1 17.2 1.0 OD2 D:ASP97 4.1 21.5 1.0 O C:HOH325 4.3 24.3 1.0 OD2 C:ASP93 4.3 20.8 1.0 OD2 D:ASP93 4.3 21.4 1.0 CG D:ASP93 4.4 20.5 1.0 OD1 D:ASP93 4.4 23.0 1.0 CG C:ASP93 4.5 20.5 1.0 OD1 C:ASP93 4.6 23.2 1.0 CG C:ASP96 4.9 18.8 1.0 CG D:ASP96 4.9 20.5 1.0 CB C:ASP96 5.0 18.3 1.0

J.I.Trujillo, J.R.Kiefer, W.Huang, J.E.Day, J.Moon, G.M.Jerome, C.P.Bono, C.M.Kornmeier, M.L.Williams, C.Kuhn, G.R.Rennie, T.A.Wynn, C.P.Carron, A.Thorarensen. Investigation of the Binding Pocket of Human Hematopoietic Prostaglandin (Pg) D2 Synthase (Hh-Pgds): A Tale of Two Waters. Bioorg.Med.Chem.Lett. V. 22 3795 2012.
ISSN: ISSN 0960-894X
PubMed: 22546671
DOI: 10.1016/J.BMCL.2012.04.004