Chlorine 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
Zinc	(Zn)	2 atoms

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

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601 b:34.7 occ:1.00 CL A:49D601 0.0 34.7 1.0 C27 A:49D601 1.7 34.4 1.0 C26 A:49D601 2.7 33.5 1.0 C28 A:49D601 2.7 34.8 1.0 CD2 A:LEU421 3.4 39.9 1.0 CB A:TYR424 3.6 38.6 1.0 CA A:MET442 3.8 43.0 1.0 CB A:MET442 3.8 43.6 1.0 CE1 A:PHE425 3.8 36.4 1.0 C25 A:49D601 4.0 34.0 1.0 C29 A:49D601 4.0 35.0 1.0 O A:PHE441 4.0 42.7 1.0 CA A:LEU421 4.2 36.0 1.0 CD1 A:PHE425 4.3 36.0 1.0 CG A:TYR424 4.3 39.8 1.0 CG1 A:VAL447 4.3 47.5 1.0 CG A:LEU421 4.5 40.1 1.0 C24 A:49D601 4.5 34.3 1.0 C A:MET442 4.6 43.0 1.0 CD1 A:TYR424 4.6 41.1 1.0 CB A:LEU421 4.6 36.9 1.0 CZ A:PHE425 4.6 35.8 1.0 O A:MET442 4.7 40.7 1.0 N A:MET442 4.8 42.8 1.0 CA A:TYR424 4.8 37.7 1.0 C A:PHE441 4.8 43.6 1.0 N A:LEU421 4.9 34.6 1.0 O A:LEU420 4.9 34.2 1.0 O A:LEU421 5.0 33.3 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601 b:38.8 occ:1.00 CL B:49D601 0.0 38.8 1.0 C27 B:49D601 1.7 37.9 1.0 C26 B:49D601 2.7 36.7 1.0 C28 B:49D601 2.7 37.6 1.0 CD2 B:LEU421 3.5 42.2 1.0 O B:PHE441 3.6 39.2 1.0 CB B:TYR424 3.7 38.6 1.0 CA B:MET442 3.9 40.4 1.0 CE1 B:PHE425 4.0 37.6 1.0 C29 B:49D601 4.0 37.2 1.0 C25 B:49D601 4.0 36.2 1.0 CA B:LEU421 4.3 37.4 1.0 CD1 B:PHE425 4.4 37.0 1.0 CG B:TYR424 4.4 38.9 1.0 CG1 B:VAL447 4.4 44.7 1.0 CB B:MET442 4.5 41.3 1.0 CG B:LEU421 4.5 41.8 1.0 C24 B:49D601 4.5 36.7 1.0 C B:PHE441 4.5 37.6 1.0 CG B:MET442 4.6 41.5 1.0 C B:MET442 4.6 41.0 1.0 CB B:LEU421 4.6 38.8 1.0 O B:MET442 4.7 41.2 1.0 N B:MET442 4.7 40.0 1.0 CZ B:PHE425 4.7 36.9 1.0 CD2 B:TYR424 4.8 41.4 1.0 CG2 B:VAL447 4.9 44.5 1.0 CA B:TYR424 4.9 37.2 1.0 CD1 B:LEU421 4.9 42.7 1.0 CB B:VAL447 5.0 44.4 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