Atomistry » Magnesium » PDB 4v26-4weo » 4wcu
Atomistry »
  Magnesium »
    PDB 4v26-4weo »
      4wcu »

Magnesium in PDB 4wcu: PDE4 Complexed with Inhibitor

Enzymatic activity of PDE4 Complexed with Inhibitor

All present enzymatic activity of PDE4 Complexed with Inhibitor:
3.1.4.53;

Protein crystallography data

The structure of PDE4 Complexed with Inhibitor, PDB code: 4wcu was solved by M.D.Sorensen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.85 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.232, 113.545, 160.535, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 30.4

Other elements in 4wcu:

The structure of PDE4 Complexed with Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PDE4 Complexed with Inhibitor (pdb code 4wcu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the PDE4 Complexed with Inhibitor, PDB code: 4wcu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4wcu

Go back to Magnesium Binding Sites List in 4wcu
Magnesium binding site 1 out of 4 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:20.6
occ:1.00
OD1 A:ASP201 2.4 24.2 1.0
O A:HOH693 2.5 19.9 1.0
CG A:ASP201 3.6 25.8 1.0
ZN A:ZN501 4.0 45.9 1.0
O A:HIS200 4.0 28.3 1.0
OD2 A:ASP201 4.0 26.2 1.0
OE2 A:GLU230 4.2 34.1 1.0
OG1 A:THR271 4.3 41.3 1.0
NE2 A:HIS233 4.3 29.4 1.0
CD2 A:HIS200 4.3 26.4 1.0
O A:HOH692 4.4 23.8 1.0
CD2 A:HIS233 4.4 27.8 1.0
C3 A:3KQ500 4.5 47.2 1.0
N4 A:3KQ500 4.5 47.0 1.0
O A:THR271 4.6 43.1 1.0
CD2 A:HIS204 4.6 30.9 1.0
OD2 A:ASP318 4.7 31.4 1.0
CG A:GLU230 4.7 33.3 1.0
CB A:THR271 4.7 41.9 1.0
NE2 A:HIS204 4.7 28.6 1.0
CB A:ASP201 4.8 26.0 1.0
NE2 A:HIS160 4.8 34.1 1.0
CD A:GLU230 4.8 33.9 1.0
CD2 A:HIS160 4.9 34.1 1.0
C A:HIS200 4.9 27.4 1.0
NE2 A:HIS200 4.9 27.4 1.0
CA A:ASP201 5.0 26.3 1.0
C2 A:3KQ500 5.0 46.5 1.0

Magnesium binding site 2 out of 4 in 4wcu

Go back to Magnesium Binding Sites List in 4wcu
Magnesium binding site 2 out of 4 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:29.6
occ:1.00
OD1 B:ASP201 2.1 30.2 1.0
CG B:ASP201 3.2 30.6 1.0
OD2 B:ASP201 3.5 32.0 1.0
ZN B:ZN501 4.0 44.0 1.0
OE2 B:GLU230 4.2 31.3 1.0
NE2 B:HIS233 4.3 31.1 1.0
O B:HIS200 4.3 31.1 1.0
OG1 B:THR271 4.3 37.1 1.0
CD2 B:HIS233 4.3 28.9 1.0
CB B:ASP201 4.5 30.8 1.0
NE2 B:HIS160 4.6 35.1 1.0
CD2 B:HIS200 4.6 32.5 1.0
ND1 B:HIS204 4.6 34.2 1.0
C3 B:3KQ500 4.6 43.3 1.0
CD2 B:HIS160 4.6 34.9 1.0
N4 B:3KQ500 4.7 44.1 1.0
CE1 B:HIS204 4.8 33.1 1.0
OD2 B:ASP318 4.8 35.7 1.0
CB B:THR271 4.8 37.7 1.0
CA B:ASP201 4.8 30.9 1.0
O B:THR271 4.9 39.1 1.0
CD B:GLU230 4.9 29.1 1.0
CG B:GLU230 4.9 28.4 1.0

Magnesium binding site 3 out of 4 in 4wcu

Go back to Magnesium Binding Sites List in 4wcu
Magnesium binding site 3 out of 4 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:26.9
occ:1.00
OD1 C:ASP201 2.2 30.8 1.0
CG C:ASP201 3.2 29.5 1.0
OD2 C:ASP201 3.5 31.2 1.0
ZN C:ZN501 3.9 48.1 1.0
NE2 C:HIS233 4.1 27.7 1.0
O C:HIS200 4.2 28.5 1.0
CD2 C:HIS233 4.3 26.7 1.0
O C:HOH629 4.3 22.1 1.0
OE2 C:GLU230 4.3 36.0 1.0
OG1 C:THR271 4.4 41.8 1.0
C3 C:3KQ500 4.5 45.3 1.0
CB C:ASP201 4.5 29.1 1.0
CD2 C:HIS200 4.6 28.7 1.0
CD2 C:HIS204 4.6 30.0 1.0
N4 C:3KQ500 4.6 45.4 1.0
OD2 C:ASP318 4.7 35.0 1.0
NE2 C:HIS204 4.7 28.4 1.0
CD2 C:HIS160 4.7 34.5 1.0
CB C:THR271 4.7 42.4 1.0
CG C:GLU230 4.8 32.4 1.0
NE2 C:HIS160 4.8 34.4 1.0
CA C:ASP201 4.8 28.9 1.0
CD C:GLU230 4.9 34.9 1.0
C2 C:3KQ500 4.9 45.3 1.0
NE2 C:HIS200 5.0 29.4 1.0

Magnesium binding site 4 out of 4 in 4wcu

Go back to Magnesium Binding Sites List in 4wcu
Magnesium binding site 4 out of 4 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PDE4 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:30.9
occ:1.00
OD1 D:ASP201 2.5 37.0 1.0
CG D:ASP201 3.6 37.7 1.0
ZN D:ZN501 3.9 50.7 1.0
OD2 D:ASP201 4.0 38.4 1.0
OG1 D:THR271 4.0 42.4 1.0
OE2 D:GLU230 4.2 34.5 1.0
C3 D:3KQ500 4.3 52.6 1.0
CD2 D:HIS200 4.4 36.6 1.0
O D:HIS200 4.4 38.1 1.0
O D:HOH647 4.4 29.3 1.0
NE2 D:HIS233 4.5 32.1 1.0
OD2 D:ASP318 4.5 42.0 1.0
O D:THR271 4.5 43.4 1.0
N4 D:3KQ500 4.6 52.4 1.0
CB D:THR271 4.6 41.9 1.0
CD2 D:HIS233 4.6 33.2 1.0
C2 D:3KQ500 4.7 52.6 1.0
NE2 D:HIS160 4.8 39.1 1.0
CG D:GLU230 4.8 32.5 1.0
CD2 D:HIS204 4.8 33.6 1.0
CD2 D:HIS160 4.8 39.3 1.0
CD D:GLU230 4.9 34.1 1.0
NE2 D:HIS200 4.9 36.4 1.0
CB D:ASP201 5.0 37.1 1.0

Reference:

J.Felding, M.D.Sorensen, T.D.Poulsen, J.Larsen, C.Andersson, P.Refer, K.Engell, L.G.Ladefoged, T.Thormann, A.M.Vinggaard, P.Hegardt, A.Sohoel, S.F.Nielsen. Discovery and Early Clinical Development of 2-{6-[2-(3,5-Dichloro-4-Pyridyl)Acetyl]-2, 3-Dimethoxyphenoxy}-N-Propylacetamide (Leo 29102), A Soft-Drug Inhibitor of Phosphodiesterase 4 For Topical Treatment of Atopic Dermatitis. J. Med. Chem. V. 57 5893 2014.
ISSN: ISSN 0022-2623
PubMed: 24984230
DOI: 10.1021/JM500378A
Page generated: Mon Dec 14 19:40:10 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