Atomistry » Magnesium » PDB 4y1p-4y8g » 4y86
Atomistry »
  Magnesium »
    PDB 4y1p-4y8g »
      4y86 »

Magnesium in PDB 4y86: Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33

Enzymatic activity of Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33

All present enzymatic activity of Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33, PDB code: 4y86 was solved by M.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.14 / 2.01
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.135, 104.135, 269.536, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 24.7

Other elements in 4y86:

The structure of Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33 also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33 (pdb code 4y86). 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 PDE9 in Complex with Racemic Inhibitor C33, PDB code: 4y86:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4y86

Go back to Magnesium Binding Sites List in 4y86
Magnesium binding site 1 out of 2 in the Crystal Structure of PDE9 in Complex with Racemic Inhibitor 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 PDE9 in Complex with Racemic Inhibitor C33 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:30.7
occ:1.00
O A:HOH718 2.0 32.2 1.0
O A:HOH722 2.2 26.7 1.0
OD1 A:ASP293 2.2 28.8 1.0
O A:HOH721 2.2 21.8 1.0
O A:HOH719 2.2 29.6 1.0
O A:HOH720 2.3 34.1 1.0
CG A:ASP293 3.2 29.6 1.0
OD2 A:ASP293 3.5 33.7 1.0
CE1 A:HIS325 3.8 23.6 1.0
ZN A:ZN602 3.9 46.8 1.0
OE2 A:GLU322 4.0 26.3 1.0
O A:HOH723 4.0 36.4 1.0
O A:HIS292 4.1 28.9 1.0
O A:HOH717 4.1 34.1 1.0
CD2 A:HIS292 4.2 33.4 1.0
OG1 A:THR363 4.2 29.1 1.0
ND1 A:HIS325 4.3 24.4 1.0
CD2 A:HIS296 4.3 27.4 1.0
CB A:ASP293 4.5 27.7 1.0
OD2 A:ASP402 4.6 31.9 1.0
NE2 A:HIS252 4.6 29.1 1.0
NE2 A:HIS296 4.7 28.1 1.0
CD2 A:HIS252 4.7 28.9 1.0
NE2 A:HIS292 4.7 36.8 1.0
CG A:GLU322 4.8 24.9 1.0
CD A:GLU322 4.8 25.9 1.0
CA A:ASP293 4.8 27.5 1.0
CB A:THR363 4.9 28.5 1.0
NE2 A:HIS325 4.9 24.0 1.0
O A:HOH771 4.9 35.0 1.0
O A:THR363 5.0 31.6 1.0
C A:HIS292 5.0 29.4 1.0

Magnesium binding site 2 out of 2 in 4y86

Go back to Magnesium Binding Sites List in 4y86
Magnesium binding site 2 out of 2 in the Crystal Structure of PDE9 in Complex with Racemic Inhibitor 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 PDE9 in Complex with Racemic Inhibitor C33 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:32.8
occ:1.00
O B:HOH724 2.0 28.6 1.0
O B:HOH727 2.0 30.9 1.0
OD1 B:ASP293 2.2 29.4 1.0
O B:HOH728 2.2 31.2 1.0
O B:HOH726 2.2 20.0 1.0
O B:HOH729 2.3 35.8 1.0
CG B:ASP293 3.2 30.5 1.0
OD2 B:ASP293 3.6 35.4 1.0
OE2 B:GLU322 3.9 28.0 1.0
NE2 B:HIS325 3.9 24.1 1.0
ZN B:ZN602 4.0 49.3 1.0
O B:HOH731 4.0 33.0 1.0
OG1 B:THR363 4.1 27.2 1.0
CD2 B:HIS325 4.1 24.1 1.0
O B:HOH725 4.2 34.4 1.0
O B:HIS292 4.2 28.8 1.0
CD2 B:HIS292 4.3 33.5 1.0
CD2 B:HIS296 4.3 28.0 1.0
CB B:ASP293 4.5 29.4 1.0
O B:HOH778 4.6 36.5 1.0
OD2 B:ASP402 4.6 34.7 1.0
NE2 B:HIS296 4.6 28.4 1.0
O B:THR363 4.7 29.4 1.0
CD B:GLU322 4.7 27.3 1.0
NE2 B:HIS292 4.7 37.3 1.0
CG B:GLU322 4.7 25.2 1.0
NE2 B:HIS252 4.7 30.0 1.0
O B:HOH764 4.8 29.9 1.0
CB B:THR363 4.8 27.8 1.0
CD2 B:HIS252 4.8 29.0 1.0
CA B:ASP293 4.9 27.7 1.0

Reference:

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
Page generated: Mon Dec 14 19:50:42 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy