Magnesium in PDB 5b25: Crystal Structure of Human PDE1B with Inhibitor 3

All present enzymatic activity of Crystal Structure of Human PDE1B with Inhibitor 3:
3.1.4.17;

The structure of Crystal Structure of Human PDE1B with Inhibitor 3, PDB code: 5b25 was solved by K.Ida, W.Lane, G.Snell, S.Sogabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.875, 102.875, 294.848, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.3

The structure of Crystal Structure of Human PDE1B with Inhibitor 3 also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Zinc	(Zn)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human PDE1B with Inhibitor 3 (pdb code 5b25). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human PDE1B with Inhibitor 3, PDB code: 5b25:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human PDE1B with Inhibitor 3


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 Human PDE1B with Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:26.1 occ:1.00 O A:HOH713 2.1 16.6 1.0 O A:HOH865 2.1 17.8 1.0 O A:HOH768 2.1 17.6 1.0 OD1 A:ASP264 2.1 17.9 1.0 O A:HOH733 2.1 15.8 1.0 O A:HOH748 2.3 20.4 1.0 CG A:ASP264 3.2 19.3 1.0 OD2 A:ASP264 3.5 19.9 1.0 ZN A:ZN601 4.0 31.2 1.0 OE2 A:GLU293 4.0 20.0 1.0 NE2 A:HIS296 4.0 18.2 1.0 O A:HIS263 4.1 18.0 1.0 OG1 A:THR334 4.2 18.8 1.0 CD2 A:HIS267 4.3 17.5 1.0 O A:HOH739 4.3 18.1 1.0 O A:HOH759 4.3 28.7 1.0 CD2 A:HIS263 4.3 14.7 1.0 CD2 A:HIS296 4.4 17.5 1.0 CB A:ASP264 4.5 16.3 1.0 O A:HOH753 4.5 44.2 1.0 NE2 A:HIS267 4.6 18.1 1.0 O A:THR334 4.7 19.4 1.0 NE2 A:HIS223 4.7 16.8 1.0 OD2 A:ASP370 4.7 23.3 1.0 CG A:GLU293 4.7 17.5 1.0 CA A:ASP264 4.8 17.8 1.0 CB A:THR334 4.8 19.6 1.0 CD A:GLU293 4.8 19.5 1.0 CD2 A:HIS223 4.8 15.8 1.0 NE2 A:HIS263 4.9 17.1 1.0 C A:HIS263 5.0 18.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human PDE1B with Inhibitor 3


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 Human PDE1B with Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:26.9 occ:1.00 O B:HOH714 2.0 17.8 1.0 O B:HOH862 2.1 17.8 1.0 O B:HOH744 2.1 16.7 1.0 O B:HOH726 2.2 20.0 1.0 OD1 B:ASP264 2.2 18.3 1.0 O B:HOH702 2.2 15.7 1.0 CG B:ASP264 3.2 18.2 1.0 OD2 B:ASP264 3.5 15.9 1.0 ZN B:ZN601 4.0 29.3 1.0 OE2 B:GLU293 4.0 19.0 1.0 NE2 B:HIS296 4.0 16.6 1.0 O B:HIS263 4.0 17.6 1.0 OG1 B:THR334 4.2 17.1 1.0 O B:HOH760 4.2 16.5 1.0 O B:HOH814 4.3 24.4 1.0 CD2 B:HIS263 4.3 13.6 1.0 CD2 B:HIS296 4.4 14.4 1.0 CD2 B:HIS267 4.4 14.7 1.0 CB B:ASP264 4.6 15.0 1.0 OD2 B:ASP370 4.6 23.2 1.0 O B:HOH728 4.6 33.9 1.0 O B:THR334 4.6 16.9 1.0 NE2 B:HIS267 4.7 14.9 1.0 CB B:THR334 4.7 16.8 1.0 NE2 B:HIS223 4.8 15.6 1.0 CG B:GLU293 4.8 15.4 1.0 CA B:ASP264 4.8 15.3 1.0 CD B:GLU293 4.8 17.5 1.0 NE2 B:HIS263 4.9 14.8 1.0 CD2 B:HIS223 4.9 15.2 1.0 C B:HIS263 5.0 15.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human PDE1B with Inhibitor 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human PDE1B with Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:26.5 occ:1.00 O C:HOH708 2.0 18.8 1.0 O C:HOH701 2.1 13.8 1.0 O C:HOH875 2.1 17.6 1.0 OD1 C:ASP264 2.2 14.6 1.0 O C:HOH781 2.2 19.7 1.0 O C:HOH728 2.3 18.9 1.0 CG C:ASP264 3.2 16.0 1.0 OD2 C:ASP264 3.4 16.4 1.0 ZN C:ZN601 3.9 29.8 1.0 O C:HIS263 4.0 16.6 1.0 OG1 C:THR334 4.1 16.2 1.0 NE2 C:HIS296 4.1 15.1 1.0 OE2 C:GLU293 4.2 19.3 1.0 O C:HOH765 4.3 18.1 1.0 CD2 C:HIS263 4.3 14.1 1.0 CD2 C:HIS296 4.4 14.4 1.0 CD2 C:HIS267 4.5 15.6 1.0 OD2 C:ASP370 4.5 20.3 1.0 CB C:ASP264 4.5 14.5 1.0 O C:HOH759 4.5 22.0 1.0 O C:THR334 4.6 17.2 1.0 CB C:THR334 4.7 16.0 1.0 O C:HOH761 4.7 34.7 1.0 NE2 C:HIS223 4.8 15.7 1.0 CG C:GLU293 4.8 17.2 1.0 CA C:ASP264 4.8 15.9 1.0 NE2 C:HIS267 4.8 15.3 1.0 NE2 C:HIS263 4.8 15.9 1.0 CD C:GLU293 4.9 19.2 1.0 C C:HIS263 4.9 16.5 1.0 CD2 C:HIS223 4.9 13.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human PDE1B with Inhibitor 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human PDE1B with Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:28.7 occ:1.00 O D:HOH732 2.0 16.6 1.0 O D:HOH863 2.1 17.6 1.0 O D:HOH703 2.2 14.3 1.0 O D:HOH755 2.2 18.6 1.0 O D:HOH726 2.2 17.9 1.0 OD1 D:ASP264 2.2 17.5 1.0 CG D:ASP264 3.2 18.2 1.0 OD2 D:ASP264 3.5 18.1 1.0 ZN D:ZN601 3.9 29.7 1.0 OE2 D:GLU293 4.1 19.5 1.0 NE2 D:HIS296 4.1 15.0 1.0 OG1 D:THR334 4.2 17.9 1.0 O D:HIS263 4.2 15.6 1.0 O D:HOH793 4.2 15.9 1.0 O D:HOH769 4.4 25.9 1.0 CD2 D:HIS263 4.4 15.2 1.0 CD2 D:HIS267 4.4 16.2 1.0 CD2 D:HIS296 4.5 14.1 1.0 O D:HOH746 4.6 34.9 1.0 OD2 D:ASP370 4.6 19.7 1.0 CB D:ASP264 4.6 16.2 1.0 O D:THR334 4.7 15.5 1.0 NE2 D:HIS223 4.7 17.7 1.0 NE2 D:HIS267 4.7 15.6 1.0 CG D:GLU293 4.7 15.9 1.0 CB D:THR334 4.7 17.2 1.0 CD D:GLU293 4.8 18.1 1.0 NE2 D:HIS263 4.8 14.7 1.0 CA D:ASP264 4.9 17.8 1.0 CD2 D:HIS223 4.9 16.0 1.0

P.Li, H.Zheng, J.Zhao, L.Zhang, W.Yao, H.Zhu, J.D.Beard, K.Ida, W.Lane, G.Snell, S.Sogabe, C.J.Heyser, G.L.Snyder, J.P.Hendrick, K.E.Vanover, R.E.Davis, L.P.Wennogle. Discovery of Potent and Selective Inhibitors of Phosphodiesterase 1 For the Treatment of Cognitive Impairment Associated with Neurodegenerative and Neuropsychiatric Diseases J.Med.Chem. V. 59 1149 2016.
ISSN: ISSN 0022-2623
PubMed: 26789933
DOI: 10.1021/ACS.JMEDCHEM.5B01751