Magnesium in PDB 2vcx: Complex Structure of Prostaglandin D2 Synthase at 2.1A.

All present enzymatic activity of Complex Structure of Prostaglandin D2 Synthase at 2.1A.:
5.3.99.2;

The structure of Complex Structure of Prostaglandin D2 Synthase at 2.1A., PDB code: 2vcx was solved by M.Hohwy, L.Spadola, B.Lundquist, K.Von Wachenfeldt, S.Persdotter, P.Hawtin, J.Dahmen, I.Groth-Clausen, R.H.A.Folmer, K.Edman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	123.813, 123.813, 106.297, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.8

The binding sites of Magnesium atom in the Complex Structure of Prostaglandin D2 Synthase at 2.1A. (pdb code 2vcx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Complex Structure of Prostaglandin D2 Synthase at 2.1A., PDB code: 2vcx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Complex Structure of Prostaglandin D2 Synthase at 2.1A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex Structure of Prostaglandin D2 Synthase at 2.1A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1200 b:21.4 occ:1.00 O A:HOH2037 2.0 10.3 1.0 O B:HOH2043 2.0 14.2 1.0 O A:HOH2036 2.0 13.8 1.0 O B:HOH2044 2.1 18.9 1.0 O B:HOH2046 2.1 12.4 1.0 O A:HOH2032 2.2 20.5 1.0 OD2 B:ASP96 3.8 10.9 1.0 OD2 A:ASP96 3.8 14.2 1.0 OD1 A:ASP97 4.0 11.6 1.0 OD1 A:ASP93 4.0 9.0 1.0 O A:HOH2035 4.1 20.2 1.0 O B:HOH2045 4.1 12.0 1.0 OD1 B:ASP97 4.2 17.0 1.0 OD1 B:ASP93 4.3 13.1 1.0 CG A:ASP93 4.3 11.2 1.0 CG B:ASP93 4.4 13.0 1.0 OD2 B:ASP93 4.5 13.4 1.0 OD2 A:ASP93 4.7 10.6 1.0 CG A:ASP96 4.8 14.4 1.0 CG B:ASP96 4.8 12.7 1.0 CB A:ASP96 4.9 12.8 1.0 CB A:ASP93 4.9 10.9 1.0 CB B:ASP96 5.0 11.0 1.0

Magnesium binding site 2 out of 2 in the Complex Structure of Prostaglandin D2 Synthase at 2.1A.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex Structure of Prostaglandin D2 Synthase at 2.1A. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1200 b:20.4 occ:1.00 O C:HOH2021 2.0 32.4 1.0 O D:HOH2025 2.0 20.4 1.0 O D:HOH2022 2.0 27.6 1.0 O C:HOH2026 2.1 21.8 1.0 O C:HOH2027 2.1 25.0 1.0 O D:HOH2028 2.2 17.0 1.0 OD2 C:ASP96 3.8 15.6 1.0 OD1 C:ASP97 3.9 21.1 1.0 OD2 D:ASP96 4.0 21.4 1.0 OD1 D:ASP97 4.1 18.0 1.0 OD1 D:ASP93 4.1 20.8 1.0 OD1 C:ASP93 4.1 16.2 1.0 O D:HOH2026 4.1 29.5 1.0 O C:HOH2025 4.2 19.0 1.0 CG C:ASP93 4.3 17.5 1.0 CG D:ASP93 4.5 20.3 1.0 OD2 C:ASP93 4.5 19.2 1.0 OD2 D:ASP93 4.8 22.8 1.0 CG C:ASP96 4.8 17.8 1.0 CG D:ASP96 4.9 20.4 1.0 CB D:ASP96 4.9 18.1 1.0 CB C:ASP96 4.9 16.9 1.0

M.Hohwy, L.Spadola, B.Lundquist, P.Hawtin, J.Dahmen, I.Groth-Clausen, E.Nilsson, S.Persdotter, K.Von Wachenfeldt, R.H.A.Folmer, K.Edman. Novel Prostaglandin D Synthase Inhibitors Generated By Fragment-Based Drug Design. J.Med.Chem. V. 51 2178 2008.
ISSN: ISSN 0022-2623
PubMed: 18341273
DOI: 10.1021/JM701509K