Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE9 in Complex with Ibmx, PDB code: 2hd1:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn101 b:41.1 occ:1.00 OD1 A:ASP402 2.1 30.9 1.0 OD2 A:ASP293 2.1 29.9 1.0 NE2 A:HIS292 2.1 31.4 1.0 NE2 A:HIS256 2.1 29.0 1.0 O A:HOH507 2.6 36.0 1.0 CD2 A:HIS292 2.9 27.1 1.0 CG A:ASP402 3.0 27.0 1.0 CD2 A:HIS256 3.1 26.6 1.0 CG A:ASP293 3.1 25.8 1.0 CE1 A:HIS256 3.1 26.1 1.0 CE1 A:HIS292 3.3 29.0 1.0 OD2 A:ASP402 3.4 26.4 1.0 OD1 A:ASP293 3.6 26.8 1.0 MG A:MG102 3.7 34.5 1.0 CG A:HIS292 4.1 25.8 1.0 CD2 A:HIS252 4.1 24.6 1.0 O A:HOH508 4.2 40.9 1.0 ND1 A:HIS256 4.2 26.6 1.0 CG A:HIS256 4.2 26.5 1.0 ND1 A:HIS292 4.3 26.5 1.0 CB A:ASP293 4.3 24.0 1.0 CB A:ASP402 4.4 26.8 1.0 O A:HOH597 4.5 37.5 1.0 NE2 A:HIS252 4.5 24.5 1.0 O A:HOH511 4.6 25.6 1.0 CG2 A:VAL260 4.7 20.5 1.0 O A:ASP402 4.8 25.9 1.0 CA A:ASP402 4.8 25.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn101 b:42.1 occ:1.00 OD1 B:ASP402 2.1 32.8 1.0 OD2 B:ASP293 2.1 30.1 1.0 NE2 B:HIS292 2.1 35.3 1.0 NE2 B:HIS256 2.1 34.9 1.0 CD2 B:HIS292 2.9 32.5 1.0 CG B:ASP402 3.0 29.6 1.0 CD2 B:HIS256 3.1 32.1 1.0 CG B:ASP293 3.1 26.9 1.0 CE1 B:HIS256 3.1 31.9 1.0 CE1 B:HIS292 3.2 33.9 1.0 OD2 B:ASP402 3.3 29.9 1.0 O B:HOH507 3.4 33.8 1.0 OD1 B:ASP293 3.6 28.1 1.0 MG B:MG102 3.7 33.5 1.0 O B:HOH508 4.0 31.7 1.0 CD2 B:HIS252 4.1 27.9 1.0 CG B:HIS292 4.1 31.3 1.0 ND1 B:HIS256 4.2 30.8 1.0 CG B:HIS256 4.2 31.5 1.0 ND1 B:HIS292 4.2 32.0 1.0 CB B:ASP293 4.3 25.8 1.0 CB B:ASP402 4.3 28.2 1.0 NE2 B:HIS252 4.4 28.3 1.0 O B:HOH583 4.6 34.7 1.0 O B:ASP402 4.6 28.4 1.0 O B:HOH511 4.6 23.3 1.0 CG2 B:VAL260 4.7 23.6 1.0 CA B:ASP402 4.8 27.8 1.0 O B:HOH509 5.0 30.1 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