Magnesium in PDB 5yx1: Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with U004

All present enzymatic activity of Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with U004:
2.5.1.18; 5.3.99.2;

The structure of Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with U004, PDB code: 5yx1 was solved by M.Kamo, N.Furubayashi, K.Inaka, K.Aritake, Y.Urade, D.Takaya, A.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.94 / 1.39
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	48.447, 47.119, 91.924, 92.20, 98.67, 90.00
R / Rfree (%)	18.5 / 21.6

The binding sites of Magnesium atom in the Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with U004 (pdb code 5yx1). 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 U004, PDB code: 5yx1:
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 U004


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 U004 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:14.9 occ:1.00 O A:HOH353 2.0 25.1 1.0 O A:HOH339 2.0 17.6 1.0 O B:HOH426 2.1 19.9 1.0 O A:HOH370 2.1 20.1 1.0 O B:HOH523 2.1 23.1 1.0 O B:HOH527 2.2 15.0 1.0 OD2 A:ASP96 3.9 19.6 1.0 OD2 A:ASP97 4.0 17.7 1.0 OD2 B:ASP96 4.0 15.3 1.0 O B:HOH552 4.1 17.2 1.0 OD2 A:ASP93 4.1 14.4 1.0 OD2 B:ASP97 4.2 15.2 1.0 OD2 B:ASP93 4.2 13.8 1.0 O A:HOH359 4.2 16.8 1.0 CG A:ASP93 4.4 13.1 1.0 CG B:ASP93 4.4 12.9 1.0 OD1 A:ASP93 4.5 14.9 1.0 OD1 B:ASP93 4.6 16.1 1.0 CG A:ASP96 4.9 17.7 1.0 CG B:ASP96 5.0 13.2 1.0 CB A:ASP96 5.0 15.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with U004


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 U004 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:15.3 occ:1.00 O C:HOH361 1.9 29.6 1.0 O D:HOH462 2.0 24.8 1.0 O C:HOH328 2.0 17.7 1.0 O D:HOH430 2.1 20.2 1.0 O D:HOH497 2.1 15.5 1.0 O C:HOH332 2.2 24.8 1.0 OD2 C:ASP96 3.9 15.9 1.0 OD2 D:ASP96 4.0 15.7 1.0 OD2 C:ASP97 4.1 17.2 1.0 OD2 D:ASP93 4.1 14.1 1.0 OD2 C:ASP93 4.1 14.2 1.0 O D:HOH459 4.2 17.4 1.0 O C:HOH379 4.2 17.5 1.0 OD2 D:ASP97 4.2 14.7 1.0 CG D:ASP93 4.3 12.4 1.0 CG C:ASP93 4.4 14.0 1.0 OD1 D:ASP93 4.4 15.6 1.0 OD1 C:ASP93 4.5 16.1 1.0 CG C:ASP96 4.9 15.5 1.0 CG D:ASP96 5.0 12.9 1.0

K.Inaka, N.Furubayashi, M.Kamo, K.Aritake, Y.Urade, D.Takaya, A.Tanaka. Crystal Structure of Hematopoietic Prostaglandin D Synthase in Complex with U004 To Be Published.