Magnesium in PDB 1v40: First Inhibitor Complex Structure of Human Hematopoietic Prostaglandin D Synthase

All present enzymatic activity of First Inhibitor Complex Structure of Human Hematopoietic Prostaglandin D Synthase:
5.3.99.2;

The structure of First Inhibitor Complex Structure of Human Hematopoietic Prostaglandin D Synthase, PDB code: 1v40 was solved by T.Inoue, Y.Okano, Y.Kado, K.Aritake, D.Irikura, N.Uodome, S.Kinugasa, N.Okazaki, H.Matsumura, Y.Kai, Y.Urade, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.05 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.288, 49.237, 94.526, 93.25, 89.98, 90.01
R / Rfree (%)	19.5 / 21.5

The binding sites of Magnesium atom in the First Inhibitor Complex Structure of Human Hematopoietic Prostaglandin D Synthase (pdb code 1v40). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the First Inhibitor Complex Structure of Human Hematopoietic Prostaglandin D Synthase, PDB code: 1v40:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the First Inhibitor Complex Structure of Human 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 First Inhibitor Complex Structure of Human Hematopoietic Prostaglandin D Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3900 b:13.9 occ:1.00 O A:HOH4290 2.0 8.4 1.0 O A:HOH4129 2.0 12.7 1.0 O D:HOH4095 2.0 17.0 1.0 O D:HOH3999 2.0 16.3 1.0 O D:HOH4096 2.0 25.5 1.0 O A:HOH4174 2.2 30.5 1.0 OD2 A:ASP96 3.9 13.7 1.0 OD2 D:ASP696 4.0 10.1 1.0 OD2 A:ASP97 4.0 13.1 1.0 OD2 D:ASP697 4.1 10.8 1.0 O D:HOH3822 4.1 6.9 1.0 OD2 D:ASP693 4.2 8.9 1.0 O A:HOH3959 4.3 14.5 1.0 OD2 A:ASP93 4.3 10.9 1.0 CG D:ASP693 4.4 9.1 1.0 O A:HOH4303 4.5 39.9 1.0 CG A:ASP93 4.5 10.7 1.0 O D:HOH3825 4.5 40.6 1.0 O D:HOH4000 4.5 35.2 1.0 OD1 D:ASP693 4.6 10.3 1.0 OD1 A:ASP93 4.6 11.8 1.0 CG A:ASP96 4.9 13.5 1.0 CG D:ASP696 5.0 9.4 1.0

Magnesium binding site 2 out of 2 in the First Inhibitor Complex Structure of Human 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 First Inhibitor Complex Structure of Human Hematopoietic Prostaglandin D Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3901 b:13.2 occ:1.00 O B:HOH4013 1.9 11.6 1.0 O C:HOH3663 2.0 23.5 1.0 O B:HOH4142 2.0 17.1 1.0 O C:HOH3625 2.1 13.2 1.0 O B:HOH4141 2.2 27.0 1.0 O C:HOH3812 2.2 19.1 1.0 OD2 B:ASP296 3.9 13.7 1.0 OD2 C:ASP496 3.9 10.4 1.0 OD2 B:ASP297 4.0 14.7 1.0 O C:HOH3623 4.1 9.4 1.0 OD2 C:ASP497 4.1 11.5 1.0 O B:HOH4042 4.1 38.3 1.0 O B:HOH3950 4.2 13.3 1.0 OD2 B:ASP293 4.2 10.8 1.0 OD2 C:ASP493 4.3 9.2 1.0 CG B:ASP293 4.4 10.4 1.0 O B:HOH4143 4.4 38.4 1.0 CG C:ASP493 4.5 8.8 1.0 OD1 B:ASP293 4.6 11.2 1.0 OD1 C:ASP493 4.7 9.8 1.0 CG B:ASP296 4.9 13.6 1.0 CG C:ASP496 4.9 9.9 1.0

T.Inoue, Y.Okano, Y.Kado, K.Aritake, D.Irikura, N.Uodome, N.Okazaki, S.Kinugasa, H.Shishitani, H.Matsumura, Y.Kai, Y.Urade. First Determination of the Inhibitor Complex Structure of Human Hematopoietic Prostaglandin D Synthase. J.Biochem.(Tokyo) V. 135 279 2004.
ISSN: ISSN 0021-924X
PubMed: 15113825
DOI: 10.1093/JB/MVH033