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Magnesium in PDB 5aix: Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.

Enzymatic activity of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.

All present enzymatic activity of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.:
2.5.1.18; 5.3.99.2;

Protein crystallography data

The structure of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor., PDB code: 5aix was solved by F.Edfeldt, J.Evenas, M.Lepisto, A.Ward, J.Petersen, L.Wissler, M.Rohman, U.Sivars, K.Svensson, M.Perry, I.Feierberg, X.Zhou, T.Hansson, F.Narjes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.65 / 2.10
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 122.228, 122.228, 106.023, 90.00, 90.00, 90.00
R / Rfree (%) 25.63 / 34.295

Other elements in 5aix:

The structure of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. (pdb code 5aix). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor., PDB code: 5aix:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5aix

Go back to Magnesium Binding Sites List in 5aix
Magnesium binding site 1 out of 2 in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1200

b:27.6
occ:1.00
O A:HOH2021 2.0 26.2 1.0
O A:HOH2022 2.2 16.2 1.0
O A:HOH2034 2.3 20.7 1.0
O A:HOH2033 2.3 16.8 1.0
O A:HOH2032 2.5 13.8 1.0
OD1 B:ASP93 3.6 23.2 1.0
OD1 A:ASP93 3.8 28.6 1.0
OD1 A:ASP97 3.9 23.9 1.0
OD2 B:ASP96 4.0 15.5 1.0
OD2 A:ASP96 4.1 14.8 1.0
O A:HOH2015 4.1 16.7 1.0
CG A:ASP93 4.3 24.5 1.0
OD1 B:ASP97 4.3 21.0 1.0
CG B:ASP93 4.3 22.2 1.0
O B:HOH2010 4.5 12.4 1.0
OD2 A:ASP93 4.7 27.9 1.0
OD2 B:ASP93 4.8 26.6 1.0
CB A:ASP96 4.8 21.0 1.0
CG A:ASP96 4.9 18.6 1.0
CB A:ASP93 4.9 22.4 1.0
CG B:ASP96 5.0 17.6 1.0
CB B:ASP96 5.0 18.0 1.0

Magnesium binding site 2 out of 2 in 5aix

Go back to Magnesium Binding Sites List in 5aix
Magnesium binding site 2 out of 2 in the Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex of Human Hematopoietic Prostagandin D2 Synthase (Hh- Pgds) in Complex with An Active Site Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1200

b:29.2
occ:1.00
O C:HOH2021 1.8 16.6 1.0
O D:HOH2007 2.1 33.6 1.0
O C:HOH2019 2.1 24.1 1.0
O D:HOH2006 2.5 18.0 1.0
OD2 D:ASP96 3.8 16.8 1.0
OD1 D:ASP97 3.9 13.2 1.0
OD2 C:ASP96 4.0 17.9 1.0
OD1 C:ASP97 4.0 20.2 1.0
OD1 D:ASP93 4.2 11.5 1.0
OD2 C:ASP93 4.4 23.5 1.0
O C:HOH2011 4.5 17.3 1.0
CG C:ASP93 4.5 19.9 1.0
CG D:ASP93 4.6 13.6 1.0
OD1 C:ASP93 4.7 15.6 1.0
OD2 D:ASP93 4.7 16.6 1.0
CG D:ASP96 4.8 17.7 1.0
CB D:ASP96 4.9 17.6 1.0
CG C:ASP96 4.9 17.7 1.0

Reference:

F.Edfeldt, J.Even, M.Lepisto, A.Ward, J.Petersen, L.Wissler, M.Rohman, U.Sivars, K.Svensson, M.Perry, I.Feierberg, X.H.Zhou, T.Hansson, F.Narjes. Identification of Indole Inhibitors of Human Hematopoietic Prostaglandin D2 Synthase (Hh-Pgds). Bioorg.Med.Chem.Lett. V. 25 2496 2015.
ISSN: ISSN 0960-894X
PubMed: 25978964
DOI: 10.1016/J.BMCL.2015.04.065
Page generated: Sun Sep 29 00:32:47 2024

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