Zinc in PDB 3dyn: Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited)

All present enzymatic activity of Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited):
3.1.4.35;

The structure of Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited), PDB code: 3dyn was solved by S.Liu, M.N.Mansour, K.Dillman, J.Perez, D.Danley, F.Menniti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.857, 103.857, 270.118, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.3

The structure of Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited) (pdb code 3dyn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited), PDB code: 3dyn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:31.9 occ:1.00 OD2 A:ASP293 2.0 32.4 1.0 OD1 A:ASP402 2.1 33.7 1.0 O A:HOH1001 2.1 41.9 1.0 NE2 A:HIS256 2.1 28.8 1.0 NE2 A:HIS292 2.2 30.1 1.0 O A:HOH1000 2.3 27.0 1.0 CD2 A:HIS292 3.0 29.7 1.0 CG A:ASP402 3.1 33.7 1.0 CD2 A:HIS256 3.1 31.4 1.0 CG A:ASP293 3.1 32.4 1.0 CE1 A:HIS256 3.1 29.4 1.0 CE1 A:HIS292 3.2 34.0 1.0 OD2 A:ASP402 3.4 34.0 1.0 OD1 A:ASP293 3.7 32.3 1.0 MG A:MG902 4.0 36.3 1.0 O1A A:PCG903 4.0 51.7 1.0 O A:HOH1028 4.0 36.6 1.0 CB A:ASP293 4.2 30.1 1.0 CG A:HIS292 4.2 29.1 1.0 CG A:HIS256 4.2 32.9 1.0 ND1 A:HIS256 4.2 31.7 1.0 CD2 A:HIS252 4.3 32.6 1.0 ND1 A:HIS292 4.3 31.7 1.0 CB A:ASP402 4.4 32.4 1.0 CG2 A:VAL260 4.5 26.3 1.0 NE2 A:HIS252 4.7 36.6 1.0 O A:ASP402 4.7 34.6 1.0 O A:HOH1003 4.9 28.1 1.0 CA A:ASP402 4.9 31.1 1.0

Zinc binding site 2 out of 2 in the Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:34.2 occ:1.00 OD1 B:ASP402 2.1 32.0 1.0 NE2 B:HIS256 2.1 27.3 1.0 OD2 B:ASP293 2.1 34.9 1.0 NE2 B:HIS292 2.2 30.2 1.0 O B:HOH904 2.4 32.0 1.0 O1A B:PCG900 2.5 35.6 0.5 CD2 B:HIS292 3.0 30.1 1.0 CD2 B:HIS256 3.1 32.2 1.0 CG B:ASP402 3.1 33.5 1.0 CE1 B:HIS256 3.1 30.2 1.0 CG B:ASP293 3.2 31.7 1.0 CE1 B:HIS292 3.3 35.1 1.0 OD2 B:ASP402 3.4 33.1 1.0 O B:HOH918 3.7 44.5 1.0 OD1 B:ASP293 3.8 33.4 1.0 PA B:PCG900 4.0 50.5 0.5 MG B:MG902 4.1 40.5 1.0 CB B:ASP293 4.2 31.4 1.0 CG B:HIS256 4.2 32.3 1.0 ND1 B:HIS256 4.2 31.7 1.0 CD2 B:HIS252 4.2 32.2 1.0 CG B:HIS292 4.2 30.1 1.0 O2A B:PCG900 4.3 36.5 0.5 ND1 B:HIS292 4.3 32.2 1.0 CB B:ASP402 4.4 32.9 1.0 O5' B:PCG900 4.6 42.7 0.5 CG2 B:VAL260 4.6 25.8 1.0 O B:ASP402 4.6 33.6 1.0 NE2 B:HIS252 4.6 36.5 1.0 CA B:ASP402 4.9 31.9 1.0 O B:HOH906 5.0 30.9 1.0

S.Liu, M.N.Mansour, K.S.Dillman, J.R.Perez, D.E.Danley, P.A.Aeed, S.P.Simons, P.K.Lemotte, F.S.Menniti. Structural Basis For the Catalytic Mechanism of Human Phosphodiesterase 9. Proc.Natl.Acad.Sci.Usa V. 105 13309 2008.
ISSN: ISSN 0027-8424
PubMed: 18757755
DOI: 10.1073/PNAS.0708850105