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Zinc in PDB 4nw7: PDE4 Catalytic Domain

Enzymatic activity of PDE4 Catalytic Domain

All present enzymatic activity of PDE4 Catalytic Domain:
3.1.4.17;

Protein crystallography data

The structure of PDE4 Catalytic Domain, PDB code: 4nw7 was solved by D.Fox Iii, T.E.Edwards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.29 / 2.15
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 98.580, 98.580, 47.570, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 20.7

Other elements in 4nw7:

The structure of PDE4 Catalytic Domain also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the PDE4 Catalytic Domain (pdb code 4nw7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the PDE4 Catalytic Domain, PDB code: 4nw7:

Zinc binding site 1 out of 1 in 4nw7

Go back to Zinc Binding Sites List in 4nw7
Zinc binding site 1 out of 1 in the PDE4 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE4 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:22.8
occ:1.00
O A:HOH959 2.0 23.4 1.0
NE2 A:HIS410 2.1 15.8 1.0
NE2 A:HIS446 2.1 19.4 1.0
OD1 A:ASP564 2.2 21.7 1.0
OD2 A:ASP447 2.2 20.2 1.0
O A:HOH914 3.0 40.9 1.0
CD2 A:HIS446 3.0 19.0 1.0
CE1 A:HIS410 3.1 15.8 1.0
CG A:ASP564 3.1 21.2 1.0
CD2 A:HIS410 3.1 15.8 1.0
CE1 A:HIS446 3.1 20.2 1.0
CG A:ASP447 3.2 18.3 1.0
OD2 A:ASP564 3.3 22.7 1.0
OD1 A:ASP447 3.7 18.6 1.0
MG A:MG702 4.0 43.7 1.0
ND1 A:HIS446 4.2 18.6 1.0
CG A:HIS446 4.2 18.0 1.0
ND1 A:HIS410 4.2 16.5 1.0
CG A:HIS410 4.2 16.5 1.0
CD2 A:HIS406 4.3 19.7 1.0
CB A:ASP447 4.4 16.2 1.0
CB A:ASP564 4.4 21.1 1.0
CG2 A:VAL414 4.5 17.2 1.0
O A:HOH886 4.6 36.2 1.0
NE2 A:HIS406 4.7 20.2 1.0
O A:HOH826 4.8 26.2 1.0
CA A:ASP564 5.0 19.4 1.0

Reference:

T.J.Hagen, X.Mo, A.B.Burgin, D.Fox, Z.Zhang, M.E.Gurney. Discovery of Triazines As Selective PDE4B Versus PDE4D Inhibitors. Bioorg.Med.Chem.Lett. V. 24 4031 2014.
ISSN: ISSN 0960-894X
PubMed: 24998378
DOI: 10.1016/J.BMCL.2014.06.002
Page generated: Wed Dec 16 05:37:45 2020

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