Zinc in PDB 4y8c: Crystal Structure of Phosphodiesterase 9 in Complex with (S)-C33

All present enzymatic activity of Crystal Structure of Phosphodiesterase 9 in Complex with (S)-C33:
3.1.4.35;

The structure of Crystal Structure of Phosphodiesterase 9 in Complex with (S)-C33, PDB code: 4y8c was solved by M.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.65 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.719, 104.719, 270.274, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.1

The structure of Crystal Structure of Phosphodiesterase 9 in Complex with (S)-C33 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Phosphodiesterase 9 in Complex with (S)-C33 (pdb code 4y8c). 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 Phosphodiesterase 9 in Complex with (S)-C33, PDB code: 4y8c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Phosphodiesterase 9 in Complex with (S)-C33


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 Phosphodiesterase 9 in Complex with (S)-C33 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:51.0 occ:1.00 OD2 A:ASP293 2.0 36.9 1.0 OD1 A:ASP402 2.1 37.6 1.0 NE2 A:HIS292 2.2 38.7 1.0 NE2 A:HIS256 2.2 40.0 1.0 O A:HOH702 2.3 36.5 1.0 O A:HOH701 2.7 39.1 1.0 CE1 A:HIS256 3.1 36.3 1.0 CD2 A:HIS292 3.1 34.6 1.0 CG A:ASP402 3.1 33.9 1.0 CG A:ASP293 3.2 31.7 1.0 CE1 A:HIS292 3.2 34.8 1.0 CD2 A:HIS256 3.2 37.4 1.0 OD2 A:ASP402 3.6 35.5 1.0 OD1 A:ASP293 3.7 33.3 1.0 MG A:MG603 3.7 32.8 1.0 CD2 A:HIS252 4.2 30.4 1.0 ND1 A:HIS256 4.2 35.3 1.0 ND1 A:HIS292 4.3 32.9 1.0 CG A:HIS292 4.3 32.6 1.0 CG A:HIS256 4.3 35.2 1.0 NE2 A:HIS252 4.3 30.2 1.0 CB A:ASP293 4.4 30.4 1.0 O A:HOH704 4.4 32.5 1.0 CB A:ASP402 4.5 34.0 1.0 O A:ASP402 4.6 32.8 1.0 O A:HOH705 4.7 21.1 1.0 CA A:ASP402 4.8 32.8 1.0 CG2 A:VAL260 4.8 30.2 1.0 O A:HOH703 5.0 17.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Phosphodiesterase 9 in Complex with (S)-C33


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 Phosphodiesterase 9 in Complex with (S)-C33 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:52.4 occ:1.00 OD2 B:ASP293 2.0 39.5 1.0 OD1 B:ASP402 2.1 36.0 1.0 NE2 B:HIS292 2.2 40.4 1.0 NE2 B:HIS256 2.2 43.5 1.0 O B:HOH701 2.4 36.3 1.0 CD2 B:HIS292 3.1 36.9 1.0 CE1 B:HIS256 3.1 39.9 1.0 CG B:ASP402 3.1 32.2 1.0 CG B:ASP293 3.1 33.7 1.0 CE1 B:HIS292 3.2 37.2 1.0 CD2 B:HIS256 3.2 41.6 1.0 OD2 B:ASP402 3.6 34.2 1.0 MG B:MG603 3.7 32.2 1.0 OD1 B:ASP293 3.7 35.2 1.0 O B:HOH702 3.9 36.6 1.0 CD2 B:HIS252 4.0 34.1 1.0 O B:HOH704 4.1 25.2 1.0 NE2 B:HIS252 4.1 34.0 1.0 ND1 B:HIS256 4.2 38.6 1.0 CG B:HIS292 4.3 35.0 1.0 ND1 B:HIS292 4.3 35.2 1.0 CB B:ASP293 4.3 32.2 1.0 CG B:HIS256 4.3 38.7 1.0 CB B:ASP402 4.4 31.6 1.0 O B:ASP402 4.5 31.4 1.0 CG2 B:VAL260 4.8 28.4 1.0 O B:HOH703 4.8 19.8 1.0 CA B:ASP402 4.8 30.6 1.0

M.Huang, Y.Shao, J.Hou, W.Cui, B.Liang, Y.Huang, Z.Li, Y.Wu, X.Zhu, P.Liu, Y.Wan, H.Ke, H.B.Luo. Structural Asymmetry of Phosphodiesterase-9A and A Unique Pocket For Selective Binding of A Potent Enantiomeric Inhibitor. Mol.Pharmacol. V. 88 836 2015.
ISSN: ESSN 1521-0111
PubMed: 26316540
DOI: 10.1124/MOL.115.099747