Magnesium in PDB 5ywe: Crystal Structure of Hematopoietic Prostaglandin D Synthase Apo Form

All present enzymatic activity of Crystal Structure of Hematopoietic Prostaglandin D Synthase Apo Form:
2.5.1.18; 5.3.99.2;

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

Resolution Low / High (Å)	88.51 / 1.68
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.429, 48.200, 88.969, 95.82, 90.08, 89.97
R / Rfree (%)	16.9 / 20.5

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

Magnesium binding site 1 out of 2 in the Crystal Structure of Hematopoietic Prostaglandin D Synthase Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:13.5 occ:1.00 O B:HOH362 2.1 18.1 1.0 O B:HOH313 2.1 27.0 1.0 O A:HOH424 2.1 22.6 1.0 O A:HOH452 2.1 15.2 1.0 O B:HOH319 2.2 18.3 1.0 O A:HOH477 2.2 15.7 1.0 OD2 B:ASP96 3.9 15.2 1.0 OD2 A:ASP96 4.0 15.0 1.0 O B:HOH346 4.0 16.4 1.0 OD2 A:ASP97 4.1 14.3 1.0 OD2 B:ASP97 4.1 14.6 1.0 O A:HOH514 4.1 36.7 1.0 OD2 A:ASP93 4.2 11.9 1.0 O A:HOH496 4.2 18.8 1.0 OD2 B:ASP93 4.2 12.8 1.0 CG A:ASP93 4.3 12.1 1.0 OD1 A:ASP93 4.4 13.4 1.0 CG B:ASP93 4.5 12.2 1.0 OD1 B:ASP93 4.7 13.7 1.0 CG B:ASP96 4.9 14.7 1.0 O A:HOH446 4.9 25.1 1.0 CG A:ASP96 5.0 14.2 1.0 CB B:ASP96 5.0 13.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Hematopoietic Prostaglandin D Synthase Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:13.0 occ:1.00 O C:HOH449 2.0 16.1 1.0 O C:HOH434 2.1 27.2 1.0 O D:HOH372 2.1 17.6 1.0 O D:HOH335 2.1 20.2 1.0 O D:HOH371 2.2 17.1 1.0 O C:HOH424 2.2 18.3 1.0 OD2 D:ASP96 3.9 14.1 1.0 OD2 C:ASP96 4.0 16.5 1.0 OD2 C:ASP97 4.0 15.8 1.0 OD2 D:ASP97 4.0 12.7 1.0 O C:HOH452 4.1 17.3 1.0 O D:HOH373 4.1 15.6 1.0 OD2 D:ASP93 4.2 12.1 1.0 OD2 C:ASP93 4.3 13.0 1.0 CG D:ASP93 4.4 12.8 1.0 CG C:ASP93 4.6 12.1 1.0 OD1 D:ASP93 4.6 14.2 1.0 OD1 C:ASP93 4.7 13.9 1.0 CG D:ASP96 4.9 13.4 1.0 CB D:ASP96 4.9 12.2 1.0 CG C:ASP96 5.0 15.7 1.0

K.Inaka, N.Furubayashi, M.Kamo, K.Aritake, Y.Urade. Crystal Structure of Hematopoietic Prostaglandin D Synthase Apo Form To Be Published.