Magnesium in PDB 2hd1: Crystal Structure of PDE9 in Complex with Ibmx

The structure of Crystal Structure of PDE9 in Complex with Ibmx, PDB code: 2hd1 was solved by Q.Huai, H.Wang, W.Zhang, R.W.Colman, H.Robinson, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.23
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.513, 103.513, 269.727, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 23.1

The structure of Crystal Structure of PDE9 in Complex with Ibmx also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE9 in Complex with Ibmx (pdb code 2hd1). 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 PDE9 in Complex with Ibmx, PDB code: 2hd1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE9 in Complex with Ibmx


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 PDE9 in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:34.5 occ:1.00 OD1 A:ASP293 2.1 26.8 1.0 O A:HOH511 2.2 25.6 1.0 O A:HOH508 2.3 40.9 1.0 O A:HOH509 2.4 25.7 1.0 O A:HOH510 2.4 24.6 1.0 CG A:ASP293 3.1 25.8 1.0 OD2 A:ASP293 3.5 29.9 1.0 ZN A:ZN101 3.7 41.1 1.0 NE2 A:HIS325 3.9 23.4 1.0 OE2 A:GLU322 3.9 23.1 1.0 CD2 A:HIS292 4.0 27.1 1.0 O A:HIS292 4.1 24.0 1.0 OG1 A:THR363 4.2 21.8 1.0 CD2 A:HIS325 4.2 22.8 1.0 O A:HOH530 4.3 26.1 1.0 O A:HOH597 4.4 37.5 1.0 CD2 A:HIS296 4.4 23.9 1.0 CB A:ASP293 4.5 24.0 1.0 O A:HOH507 4.5 36.0 1.0 NE2 A:HIS292 4.5 31.4 1.0 CD2 A:HIS252 4.5 24.6 1.0 OD2 A:ASP402 4.6 26.4 1.0 NE2 A:HIS296 4.7 24.3 1.0 CA A:ASP293 4.7 24.4 1.0 NE2 A:HIS252 4.8 24.5 1.0 CB A:THR363 4.8 21.9 1.0 CD A:GLU322 4.8 23.3 1.0 C A:HIS292 4.9 23.3 1.0 CG A:GLU322 5.0 22.2 1.0 OD1 A:ASP402 5.0 30.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE9 in Complex with Ibmx


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 PDE9 in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:33.5 occ:1.00 OD1 B:ASP293 2.1 28.1 1.0 O B:HOH508 2.2 31.7 1.0 O B:HOH511 2.3 23.3 1.0 O B:HOH509 2.3 30.1 1.0 O B:HOH510 2.3 26.2 1.0 CG B:ASP293 3.0 26.9 1.0 OD2 B:ASP293 3.3 30.1 1.0 ZN B:ZN101 3.7 42.1 1.0 OE2 B:GLU322 4.0 27.3 1.0 O B:HOH583 4.0 34.7 1.0 NE2 B:HIS325 4.1 22.9 1.0 O B:HOH514 4.1 28.2 1.0 CD2 B:HIS292 4.2 32.5 1.0 CD2 B:HIS296 4.2 26.5 1.0 O B:HOH562 4.2 35.0 1.0 CD2 B:HIS252 4.4 27.9 1.0 CD2 B:HIS325 4.4 22.9 1.0 OG1 B:THR363 4.4 23.0 1.0 O B:HIS292 4.4 25.7 1.0 CB B:ASP293 4.4 25.8 1.0 NE2 B:HIS252 4.4 28.3 1.0 NE2 B:HIS296 4.5 26.4 1.0 NE2 B:HIS292 4.6 35.3 1.0 OD2 B:ASP402 4.6 29.9 1.0 O B:HOH546 4.8 35.7 1.0 CA B:ASP293 4.8 26.0 1.0 O B:HOH522 4.9 26.8 1.0 CD B:GLU322 4.9 25.7 1.0 CB B:THR363 5.0 23.7 1.0 O B:THR363 5.0 26.1 1.0

Q.Huai, H.Wang, W.Zhang, R.W.Colman, H.Robinson, H.Ke. Crystal Structure of Phosphodiesterase 9 Shows Orientation Variation of Inhibitor Ibmx Binding Proc.Natl.Acad.Sci.Usa V. 101 9624 2004.
ISSN: ISSN 0027-8424
PubMed: 15210993
DOI: 10.1073/PNAS.0401120101