Atomistry » Magnesium » PDB 4fs5-4g7f » 4g2l
Atomistry »
  Magnesium »
    PDB 4fs5-4g7f »
      4g2l »

Magnesium in PDB 4g2l: Human PDE9 in Complex with Selective Compound

Enzymatic activity of Human PDE9 in Complex with Selective Compound

All present enzymatic activity of Human PDE9 in Complex with Selective Compound:
3.1.4.35;

Protein crystallography data

The structure of Human PDE9 in Complex with Selective Compound, PDB code: 4g2l was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.81 / 3.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.226, 104.226, 270.476, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.4

Other elements in 4g2l:

The structure of Human PDE9 in Complex with Selective Compound also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human PDE9 in Complex with Selective Compound (pdb code 4g2l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human PDE9 in Complex with Selective Compound, PDB code: 4g2l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4g2l

Go back to Magnesium Binding Sites List in 4g2l
Magnesium binding site 1 out of 2 in the Human PDE9 in Complex with Selective Compound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human PDE9 in Complex with Selective Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:36.3
occ:1.00
OD1 A:ASP293 2.3 22.7 1.0
CG A:ASP293 3.4 25.5 1.0
NE2 A:HIS325 3.8 26.7 1.0
OD2 A:ASP293 3.8 25.2 1.0
ZN A:ZN901 3.9 40.7 1.0
O A:HIS292 4.0 26.9 1.0
CD2 A:HIS325 4.1 24.7 1.0
OG1 A:THR363 4.1 22.7 1.0
OE2 A:GLU322 4.2 28.0 1.0
CD2 A:HIS292 4.2 26.9 1.0
CD2 A:HIS296 4.5 29.9 1.0
CG A:GLU322 4.6 23.9 1.0
CB A:ASP293 4.7 26.5 1.0
CB A:THR363 4.7 23.0 1.0
CD A:GLU322 4.8 25.6 1.0
NE2 A:HIS292 4.8 28.4 1.0
OD2 A:ASP402 4.8 27.8 1.0
NE2 A:HIS252 4.9 29.3 1.0
CA A:ASP293 4.9 26.0 1.0
O A:THR363 4.9 26.1 1.0
NE2 A:HIS296 4.9 31.5 1.0
C A:HIS292 4.9 26.1 1.0
CD2 A:HIS252 5.0 28.7 1.0

Magnesium binding site 2 out of 2 in 4g2l

Go back to Magnesium Binding Sites List in 4g2l
Magnesium binding site 2 out of 2 in the Human PDE9 in Complex with Selective Compound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human PDE9 in Complex with Selective Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:26.1
occ:1.00
OD1 B:ASP293 2.3 23.6 1.0
CG B:ASP293 3.3 25.6 1.0
OD2 B:ASP293 3.7 26.0 1.0
NE2 B:HIS325 3.9 25.7 1.0
ZN B:ZN901 3.9 44.1 1.0
OE2 B:GLU322 4.0 29.2 1.0
CD2 B:HIS325 4.1 25.5 1.0
OG1 B:THR363 4.2 24.4 1.0
CD2 B:HIS292 4.2 27.3 1.0
O B:HIS292 4.2 26.7 1.0
CD2 B:HIS296 4.5 28.4 1.0
CG B:GLU322 4.6 24.5 1.0
CB B:ASP293 4.7 26.0 1.0
OD2 B:ASP402 4.7 27.4 1.0
NE2 B:HIS252 4.7 30.3 1.0
NE2 B:HIS296 4.8 27.9 1.0
NE2 B:HIS292 4.8 29.5 1.0
CD B:GLU322 4.8 26.1 1.0
CD2 B:HIS252 4.8 28.3 1.0
CB B:THR363 4.9 23.2 1.0
CE1 B:HIS325 4.9 25.8 1.0
CA B:ASP293 4.9 25.7 1.0

Reference:

M.M.Claffey, C.J.Helal, P.R.Verhoest, Z.Kang, K.S.Fors, S.Jung, J.Zhong, M.W.Bundesmann, X.Hou, S.Lui, R.J.Kleiman, M.Vanase-Frawley, A.W.Schmidt, F.Menniti, C.J.Schmidt, W.E.Hoffman, M.Hajos, L.Mcdowell, R.E.O'connor, M.Macdougall-Murphy, K.R.Fonseca, S.L.Becker, F.R.Nelson, S.Liras. Application of Structure-Based Drug Design and Parallel Chemistry to Identify Selective, Brain Penetrant, in Vivo Active Phosphodiesterase 9A Inhibitors. J.Med.Chem. V. 55 9055 2012.
ISSN: ISSN 0022-2623
PubMed: 23025719
DOI: 10.1021/JM3009635
Page generated: Mon Dec 14 15:54:34 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy