Atomistry » Zinc » PDB 4q8x-4qhp » 4qge
Atomistry »
  Zinc »
    PDB 4q8x-4qhp »
      4qge »

Zinc in PDB 4qge: Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D

Protein crystallography data

The structure of Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D, PDB code: 4qge was solved by Y.-X.Shao, M.Huang, W.Cui, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.580, 103.580, 268.657, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 26.8

Other elements in 4qge:

The structure of Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D (pdb code 4qge). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D, PDB code: 4qge:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4qge

Go back to Zinc Binding Sites List in 4qge
Zinc binding site 1 out of 2 in the Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:38.1
occ:1.00
OD2 A:ASP293 2.1 28.1 1.0
OD1 A:ASP402 2.1 30.7 1.0
NE2 A:HIS256 2.1 29.5 1.0
NE2 A:HIS292 2.1 26.1 1.0
O A:HOH702 2.4 27.1 1.0
O A:HOH701 2.5 26.6 1.0
CD2 A:HIS292 3.0 21.9 1.0
CE1 A:HIS256 3.1 22.3 1.0
CG A:ASP402 3.1 28.0 1.0
CD2 A:HIS256 3.1 22.2 1.0
CG A:ASP293 3.1 25.0 1.0
CE1 A:HIS292 3.2 24.1 1.0
OD2 A:ASP402 3.5 30.1 1.0
OD1 A:ASP293 3.7 23.8 1.0
MG A:MG603 3.8 28.0 1.0
O A:HOH745 4.1 26.4 1.0
CD2 A:HIS252 4.1 23.1 1.0
CG A:HIS292 4.2 23.8 1.0
ND1 A:HIS256 4.2 24.1 1.0
ND1 A:HIS292 4.2 22.4 1.0
CG A:HIS256 4.2 24.3 1.0
CB A:ASP293 4.3 23.5 1.0
O A:HOH704 4.3 28.7 1.0
NE2 A:HIS252 4.4 23.1 1.0
CB A:ASP402 4.4 27.8 1.0
O A:ASP402 4.6 26.9 1.0
O A:HOH705 4.8 16.8 1.0
CG2 A:VAL260 4.8 20.1 1.0
CA A:ASP402 4.8 27.6 1.0

Zinc binding site 2 out of 2 in 4qge

Go back to Zinc Binding Sites List in 4qge
Zinc binding site 2 out of 2 in the Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:41.9
occ:1.00
OD2 B:ASP293 2.0 30.7 1.0
OD1 B:ASP402 2.1 30.1 1.0
NE2 B:HIS292 2.1 31.6 1.0
NE2 B:HIS256 2.1 31.4 1.0
O B:HOH701 2.3 34.9 1.0
O B:HOH702 2.4 23.8 1.0
CD2 B:HIS292 2.9 26.9 1.0
CE1 B:HIS256 3.1 27.0 1.0
CG B:ASP402 3.1 26.7 1.0
CD2 B:HIS256 3.1 25.6 1.0
CG B:ASP293 3.2 28.3 1.0
CE1 B:HIS292 3.2 29.2 1.0
OD2 B:ASP402 3.5 31.2 1.0
OD1 B:ASP293 3.7 29.9 1.0
MG B:MG603 3.8 29.0 1.0
CD2 B:HIS252 4.1 24.3 1.0
CG B:HIS292 4.1 26.9 1.0
O B:HOH716 4.2 31.5 1.0
ND1 B:HIS256 4.2 27.8 1.0
ND1 B:HIS292 4.2 27.8 1.0
CG B:HIS256 4.2 27.2 1.0
CB B:ASP293 4.3 23.6 1.0
NE2 B:HIS252 4.3 23.1 1.0
O B:HOH704 4.3 31.1 1.0
CB B:ASP402 4.4 26.8 1.0
O B:HOH773 4.5 44.3 1.0
O B:ASP402 4.6 25.1 1.0
O B:HOH703 4.7 18.4 1.0
CG2 B:VAL260 4.8 26.3 1.0
CA B:ASP402 4.8 26.0 1.0

Reference:

Y.X.Shao, M.Huang, W.Cui, L.J.Feng, Y.Wu, Y.Cai, Z.Li, X.Zhu, P.Liu, Y.Wan, H.Ke, H.B.Luo. Discovery of A Phosphodiesterase-9A Inhibitor As A Potential Hypoglycemic Agent. J.Med.Chem. 2014.
ISSN: ISSN 0022-2623
PubMed: 25432025
DOI: 10.1021/JM500836H
Page generated: Sun Oct 27 06:32:54 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy