Magnesium in PDB 5y9z: Crystal Structure of Rat Hematopoietic Prostaglandin D Synthase

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

The structure of Crystal Structure of Rat Hematopoietic Prostaglandin D Synthase, PDB code: 5y9z was solved by M.Kamo, N.Furubayashi, K.Inaka, H.Tanaka, K.Aritake, Y.Urade, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.30 / 1.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.540, 79.840, 96.600, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 17.9

The binding sites of Magnesium atom in the Crystal Structure of Rat Hematopoietic Prostaglandin D Synthase (pdb code 5y9z). 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 Rat Hematopoietic Prostaglandin D Synthase, PDB code: 5y9z:
Jump to Magnesium binding site number: 1; 2;

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


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 Rat Hematopoietic Prostaglandin D Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:7.5 occ:1.00 O B:HOH343 2.0 18.9 1.0 O A:HOH321 2.0 19.1 1.0 O B:HOH341 2.1 9.4 1.0 O B:HOH349 2.1 10.6 1.0 O A:HOH353 2.1 8.2 1.0 O A:HOH341 2.1 10.9 1.0 OD2 A:ASP96 4.0 10.5 1.0 OD2 B:ASP96 4.0 9.0 1.0 OD1 A:ASP97 4.0 8.5 1.0 O A:HOH512 4.1 18.2 1.0 O A:HOH415 4.1 9.6 1.0 OD1 B:ASP97 4.1 9.4 1.0 O B:HOH373 4.1 8.0 1.0 OD1 A:ASP93 4.1 7.4 1.0 OD1 B:ASP93 4.2 7.4 1.0 CG A:ASP93 4.3 6.4 1.0 CG B:ASP93 4.4 6.8 1.0 OD2 A:ASP93 4.5 8.1 1.0 OD2 B:ASP93 4.5 8.2 1.0 CG B:ASP96 4.9 7.3 1.0 CG A:ASP96 4.9 7.1 1.0

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


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 Rat Hematopoietic Prostaglandin D Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:14.8 occ:1.00 O A:HOH381 2.0 14.5 1.0 O A:HOH386 2.0 16.0 1.0 O A:HOH563 2.1 17.0 1.0 O A:HOH390 2.1 14.2 1.0 O A:HOH532 2.1 17.1 1.0 O A:HOH513 2.1 14.6 1.0 O A:HOH495 4.0 23.3 1.0 O A:HOH322 4.1 8.6 1.0 O A:LYS138 4.2 7.2 1.0 OE2 A:GLU139 4.2 16.0 1.0 NZ A:LYS180 4.2 12.2 1.0 OE1 A:GLU139 4.2 16.5 1.0 O A:ASP137 4.3 9.8 1.0 O A:HOH391 4.3 15.2 1.0 O A:HOH459 4.4 16.6 1.0 CD A:GLU139 4.5 13.1 1.0 O A:HOH503 4.9 22.1 1.0 C A:LYS138 4.9 6.9 1.0 CA A:GLU139 4.9 7.3 1.0 C A:ASP137 5.0 8.6 1.0

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