Magnesium 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:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	2 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603 b:32.8 occ:1.00 O A:HOH702 1.8 36.5 1.0 O A:HOH706 2.1 25.5 1.0 OD1 A:ASP293 2.2 33.3 1.0 O A:HOH703 2.2 17.2 1.0 O A:HOH705 2.2 21.1 1.0 O A:HOH704 2.3 32.5 1.0 CG A:ASP293 3.1 31.7 1.0 OD2 A:ASP293 3.4 36.9 1.0 ZN A:ZN602 3.7 51.0 1.0 CE1 A:HIS325 3.9 26.3 1.0 OE2 A:GLU322 4.0 28.4 1.0 CD2 A:HIS292 4.1 34.6 1.0 O A:HIS292 4.2 28.5 1.0 O A:HOH701 4.3 39.1 1.0 ND1 A:HIS325 4.3 26.6 1.0 CD2 A:HIS296 4.3 29.3 1.0 OG1 A:THR363 4.4 24.0 1.0 NE2 A:HIS292 4.4 38.7 1.0 CB A:ASP293 4.5 30.4 1.0 NE2 A:HIS252 4.6 30.2 1.0 NE2 A:HIS296 4.7 29.2 1.0 CD2 A:HIS252 4.7 30.4 1.0 OD2 A:ASP402 4.7 35.5 1.0 CG A:GLU322 4.8 28.4 1.0 CD A:GLU322 4.8 29.3 1.0 CA A:ASP293 4.8 29.6 1.0 CB A:THR363 4.9 25.7 1.0 OD1 A:ASP402 5.0 37.6 1.0 NE2 A:HIS325 5.0 27.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603 b:32.2 occ:1.00 O B:HOH701 1.9 36.3 1.0 O B:HOH705 2.0 27.0 1.0 OD1 B:ASP293 2.2 35.2 1.0 O B:HOH704 2.2 25.2 1.0 O B:HOH703 2.3 19.8 1.0 O B:HOH706 2.4 32.6 1.0 CG B:ASP293 3.1 33.7 1.0 OD2 B:ASP293 3.3 39.5 1.0 ZN B:ZN602 3.7 52.4 1.0 NE2 B:HIS325 4.0 26.3 1.0 OE2 B:GLU322 4.0 26.5 1.0 CD2 B:HIS292 4.1 36.9 1.0 CD2 B:HIS325 4.2 25.7 1.0 O B:HIS292 4.3 34.4 1.0 CD2 B:HIS296 4.3 28.2 1.0 OG1 B:THR363 4.3 25.5 1.0 NE2 B:HIS292 4.4 40.4 1.0 CB B:ASP293 4.5 32.2 1.0 NE2 B:HIS252 4.5 34.0 1.0 NE2 B:HIS296 4.6 27.9 1.0 CD2 B:HIS252 4.7 34.1 1.0 OD2 B:ASP402 4.7 34.2 1.0 O B:THR363 4.9 25.8 1.0 CA B:ASP293 4.9 31.1 1.0 OD1 B:ASP402 4.9 36.0 1.0 CB B:THR363 4.9 25.8 1.0 CD B:GLU322 4.9 27.4 1.0 CG B:GLU322 4.9 26.8 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