Calcium in PDB 1iyi: 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: 1iyi was solved by T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.29 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.784, 47.263, 183.810, 90.00, 97.83, 90.00
R / Rfree (%)	18.8 / 22

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

Calcium 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 Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Hematopoietic Prostaglandin D Synthase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1901 b:29.7 occ:1.00 O B:HOH1432 2.1 24.2 1.0 O B:HOH1473 2.4 22.3 1.0 O C:HOH1989 2.4 18.7 1.0 O C:HOH2004 2.5 18.0 1.0 O C:HOH1988 2.6 24.1 1.0 OD2 C:ASP496 2.8 14.4 1.0 O B:HOH1433 2.8 21.4 1.0 O C:HOH2005 3.8 18.8 1.0 CG C:ASP496 3.9 13.9 1.0 OD2 B:ASP296 4.0 14.9 1.0 O B:HOH1550 4.1 33.6 1.0 OD2 B:ASP297 4.2 13.6 1.0 OD2 C:ASP497 4.2 13.3 1.0 CB C:ASP496 4.3 12.8 1.0 O B:HOH1431 4.4 17.2 1.0 OD2 C:ASP493 4.4 14.2 1.0 OD2 B:ASP293 4.5 12.9 1.0 CG B:ASP293 4.6 12.8 1.0 CG C:ASP493 4.7 13.6 1.0 OD1 B:ASP293 4.7 13.3 1.0 CD1 C:LEU465 4.9 11.2 1.0 OD1 C:ASP496 5.0 15.8 1.0

Calcium 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 Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Hematopoietic Prostaglandin D Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1900 b:24.1 occ:1.00 O A:HOH1437 2.1 23.3 1.0 O D:HOH2030 2.3 18.5 1.0 O A:HOH1259 2.4 17.8 1.0 O D:HOH1908 2.5 15.1 1.0 O D:HOH2009 2.5 12.8 1.0 OD2 D:ASP696 2.8 14.0 1.0 O A:HOH1284 2.8 18.6 1.0 O D:HOH1910 3.8 21.7 1.0 CG D:ASP696 3.9 12.7 1.0 O D:HOH2114 3.9 42.2 1.0 OD2 A:ASP96 4.1 11.9 1.0 OD2 D:ASP693 4.2 11.4 1.0 OD2 D:ASP697 4.2 11.0 1.0 OD2 A:ASP97 4.2 11.4 1.0 O A:HOH1417 4.3 38.2 1.0 CB D:ASP696 4.3 11.6 1.0 OD2 A:ASP93 4.5 10.7 1.0 CG D:ASP693 4.5 11.3 1.0 O A:HOH1257 4.6 16.9 1.0 CG A:ASP93 4.6 10.6 1.0 OD1 A:ASP93 4.6 11.9 1.0 O A:HOH1484 4.8 45.8 1.0 OD1 D:ASP693 4.9 12.2 1.0 CD1 D:LEU665 4.9 10.3 1.0 OD1 D:ASP696 4.9 14.6 1.0 O D:HOH2133 4.9 34.2 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