Magnesium in PDB 5ywx: Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with F092

All present enzymatic activity of Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with F092:
2.5.1.18; 5.3.99.2;

The structure of Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with F092, PDB code: 5ywx was solved by M.Kamo, N.Furubayashi, K.Inaka, K.Aritake, A.Omura, A.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.04 / 1.74
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.040, 48.170, 92.110, 98.97, 92.34, 90.01
R / Rfree (%)	20.3 / 25.3

The binding sites of Magnesium atom in the Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with F092 (pdb code 5ywx). 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 Hematopoietic Prostaglandin D Synthase in Complex with F092, PDB code: 5ywx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with F092


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 Hematopoietic Prostaglandin D Synthase in Complex with F092 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:19.2 occ:1.00 O B:HOH304 1.9 27.4 1.0 O B:HOH322 2.0 23.0 1.0 O A:HOH488 2.0 24.1 1.0 O A:HOH456 2.2 23.4 1.0 O B:HOH329 2.2 19.6 1.0 O A:HOH529 2.2 24.6 1.0 OD2 B:ASP96 3.8 18.2 1.0 O B:HOH328 3.9 18.9 1.0 OD2 A:ASP97 4.0 14.5 1.0 OD2 B:ASP93 4.1 13.5 1.0 OD2 B:ASP97 4.1 23.1 1.0 O A:HOH561 4.1 38.9 1.0 OD2 A:ASP96 4.2 13.0 1.0 O A:HOH461 4.2 23.9 1.0 OD2 A:ASP93 4.3 16.0 1.0 CG A:ASP93 4.4 13.6 1.0 CG B:ASP93 4.5 14.2 1.0 OD1 A:ASP93 4.5 17.4 1.0 CG B:ASP96 4.7 17.9 1.0 OD1 B:ASP93 4.8 15.1 1.0 CB B:ASP96 4.8 16.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with F092


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 Hematopoietic Prostaglandin D Synthase in Complex with F092 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:21.0 occ:1.00 O C:HOH334 2.0 23.8 1.0 O C:HOH322 2.0 16.4 1.0 O C:HOH329 2.1 28.6 1.0 O D:HOH485 2.1 22.6 1.0 O D:HOH452 2.2 19.6 1.0 O D:HOH483 2.3 25.2 1.0 OD2 C:ASP96 3.8 17.2 1.0 OD2 D:ASP96 3.9 13.2 1.0 O D:HOH564 3.9 33.7 1.0 OD2 C:ASP97 4.0 20.6 1.0 O D:HOH430 4.0 22.4 1.0 OD2 D:ASP97 4.0 14.8 1.0 O C:HOH325 4.1 28.8 1.0 OD2 C:ASP93 4.2 12.5 1.0 OD2 D:ASP93 4.4 15.5 1.0 CG C:ASP93 4.6 12.3 1.0 CG D:ASP93 4.6 14.7 1.0 OD1 D:ASP93 4.8 19.0 1.0 CG C:ASP96 4.8 18.3 1.0 OD1 C:ASP93 4.8 13.2 1.0 CG D:ASP96 4.9 12.2 1.0 CB C:ASP96 5.0 17.1 1.0

D.Takaya, K.Inaka, A.Omura, K.Takenuki, M.Kawanishi, Y.Yabuki, Y.Nakagawa, K.Tsuganezawa, N.Ogawa, C.Watanabe, T.Honma, K.Aritake, Y.Urade, M.Shirouzu, A.Tanaka. Characterization of Crystal Water Molecules in A High-Affinity Inhibitor and Hematopoietic Prostaglandin D Synthase Complex By Interaction Energy Studies. Bioorg. Med. Chem. V. 26 4726 2018.
ISSN: ESSN 1464-3391
PubMed: 30121213
DOI: 10.1016/J.BMC.2018.08.014