Magnesium in PDB 1iyh: Crystal Structure of Hematopoietic Prostaglandin D Synthase

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

The structure of Crystal Structure of Hematopoietic Prostaglandin D Synthase, PDB code: 1iyh was solved by T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.94 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.113, 47.373, 184.696, 90.00, 97.44, 90.00
R / Rfree (%)	20.5 / 23.8

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

Magnesium binding site 1 out of 2 in the Crystal Structure of 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 Hematopoietic Prostaglandin D Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1901 b:22.3 occ:1.00 O A:HOH1903 2.1 28.3 1.0 O A:HOH1902 2.1 23.7 1.0 O C:HOH1602 2.2 23.5 1.0 O C:HOH1603 2.2 25.2 1.0 O C:HOH1601 2.2 29.3 1.0 O A:HOH1904 2.2 22.3 1.0 OD2 A:ASP96 3.9 21.1 1.0 OD2 C:ASP496 3.9 20.2 1.0 OD2 C:ASP497 4.0 20.7 1.0 OD2 A:ASP97 4.1 19.4 1.0 O C:HOH1677 4.1 30.0 1.0 O A:HOH1984 4.2 25.9 1.0 OD2 A:ASP93 4.3 20.8 1.0 OD2 C:ASP493 4.3 19.2 1.0 CG A:ASP93 4.5 19.7 1.0 CG C:ASP493 4.6 18.4 1.0 OD1 A:ASP93 4.6 21.5 1.0 O C:HOH1696 4.6 37.2 1.0 OD1 C:ASP493 4.7 19.5 1.0 O C:HOH1719 4.9 35.3 1.0 CG A:ASP96 4.9 19.8 1.0 CG C:ASP496 5.0 19.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 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 Hematopoietic Prostaglandin D Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1902 b:23.4 occ:1.00 O D:HOH1802 2.0 25.7 1.0 O B:HOH1904 2.0 25.8 1.0 O D:HOH1801 2.1 37.5 1.0 O B:HOH1903 2.1 27.9 1.0 O D:HOH1803 2.2 23.3 1.0 O B:HOH1905 2.2 22.2 1.0 OD2 B:ASP296 3.9 19.3 1.0 OD2 D:ASP696 3.9 19.8 1.0 OD2 D:ASP697 4.0 20.2 1.0 OD2 B:ASP297 4.0 20.1 1.0 O B:HOH2076 4.0 40.9 1.0 O B:HOH2111 4.2 19.9 1.0 O D:HOH1919 4.2 31.9 1.0 OD2 B:ASP293 4.3 19.2 1.0 OD2 D:ASP693 4.4 19.5 1.0 CG B:ASP293 4.5 18.9 1.0 CG D:ASP693 4.6 18.5 1.0 OD1 B:ASP293 4.7 19.6 1.0 OD1 D:ASP693 4.7 20.1 1.0 CG D:ASP696 4.9 19.4 1.0 CG B:ASP296 4.9 18.6 1.0

T.Inoue, D.Irikura, N.Okazaki, S.Kinugasa, H.Matsumura, N.Uodome, M.Yamamoto, T.Kumasaka, M.Miyano, Y.Kai, Y.Urade. Mechanism of Metal Activation of Human Hematopoietic Prostaglandin D Synthase Nat.Struct.Biol. V. 10 291 2003.
ISSN: ISSN 1072-8368
PubMed: 12627223
DOI: 10.1038/NSB907