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Zinc in PDB 3d3p: Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor

Enzymatic activity of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor

All present enzymatic activity of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor, PDB code: 3d3p was solved by D.O.Somers, M.Neu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.75
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.448, 94.725, 105.671, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.1

Other elements in 3d3p:

The structure of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Arsenic (As) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor (pdb code 3d3p). 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 Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor, PDB code: 3d3p:

Zinc binding site 1 out of 1 in 3d3p

Go back to Zinc Binding Sites List in 3d3p
Zinc binding site 1 out of 1 in the Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PDE4B Catalytic Domain in Complex with A Pyrazolopyridine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:20.2
occ:1.00
 OD2 A:ASP275 2.2 15.4 1.0
NE2 A:HIS238 2.2 17.3 1.0
OD1 A:ASP392 2.2 16.6 1.0
NE2 A:HIS274 2.2 15.7 1.0
O A:HOH580 2.3 20.8 1.0
O A:HOH668 2.3 16.7 1.0
CG A:ASP392 3.1 22.6 1.0
CD2 A:HIS274 3.1 16.4 1.0
CD2 A:HIS238 3.1 17.9 1.0
CG A:ASP275 3.1 14.6 1.0
CE1 A:HIS238 3.2 12.2 1.0
CE1 A:HIS274 3.2 22.1 1.0
OD2 A:ASP392 3.3 21.9 1.0
OD1 A:ASP275 3.6 15.3 1.0
MG A:MG504 3.8 20.3 1.0
O A:HOH584 4.0 19.3 1.0
CD2 A:HIS234 4.2 21.4 1.0
O A:HOH667 4.2 19.2 1.0
CG A:HIS274 4.2 14.3 1.0
CG A:HIS238 4.3 16.7 1.0
CB A:ASP275 4.3 12.9 1.0
ND1 A:HIS274 4.3 14.9 1.0
ND1 A:HIS238 4.3 18.7 1.0
NE2 A:HIS234 4.4 20.7 1.0
CB A:ASP392 4.4 17.9 1.0
CG2 A:VAL242 4.8 17.8 1.0
O A:HOH581 4.8 18.2 1.0
CA A:ASP392 4.9 17.1 1.0

Reference:

J.N.Hamblin, T.D.Angell, S.P.Ballantine, C.M.Cook, A.W.Cooper, J.Dawson, C.J.Delves, P.S.Jones, M.Lindvall, F.S.Lucas, C.J.Mitchell, M.Y.Neu, L.E.Ranshaw, Y.E.Solanke, D.O.Somers, J.O.Wiseman. Pyrazolopyridines As A Novel Structural Class of Potent and Selective PDE4 Inhibitors. Bioorg.Med.Chem.Lett. V. 18 4237 2008.
ISSN: ISSN 0960-894X
PubMed: 18539455
DOI: 10.1016/J.BMCL.2008.05.052
Page generated: Thu Oct 24 12:02:05 2024

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