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Zinc in PDB 3bjc: Crystal Structure of the PDE5A Catalytic Domain in Complex with A Novel Inhibitor

Enzymatic activity of Crystal Structure of the PDE5A Catalytic Domain in Complex with A Novel Inhibitor

All present enzymatic activity of Crystal Structure of the PDE5A Catalytic Domain in Complex with A Novel Inhibitor:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the PDE5A Catalytic Domain in Complex with A Novel Inhibitor, PDB code: 3bjc was solved by G.Chen, H.Wang, R.Howard, J.Cai, Y.Wan, 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 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.755, 73.755, 132.509, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 22.1

Other elements in 3bjc:

The structure of Crystal Structure of the PDE5A Catalytic Domain in Complex with A Novel Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the PDE5A Catalytic Domain in Complex with A Novel Inhibitor (pdb code 3bjc). 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 the PDE5A Catalytic Domain in Complex with A Novel Inhibitor, PDB code: 3bjc:

Zinc binding site 1 out of 1 in 3bjc

Go back to Zinc Binding Sites List in 3bjc
Zinc binding site 1 out of 1 in the Crystal Structure of the PDE5A Catalytic Domain in Complex with A Novel 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 the PDE5A Catalytic Domain in Complex with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn876

b:30.4
occ:1.00
OD2 A:ASP654 2.1 33.0 1.0
OD1 A:ASP764 2.1 30.5 1.0
NE2 A:HIS653 2.2 26.9 1.0
NE2 A:HIS617 2.2 20.8 1.0
O A:HOH903 2.2 26.8 1.0
CD2 A:HIS653 3.0 26.4 1.0
CG A:ASP764 3.0 29.7 1.0
CD2 A:HIS617 3.0 23.8 1.0
CG A:ASP654 3.1 30.8 1.0
OD2 A:ASP764 3.3 32.1 1.0
CE1 A:HIS617 3.3 23.6 1.0
CE1 A:HIS653 3.3 28.1 1.0
OD1 A:ASP654 3.6 36.0 1.0
O A:HOH902 3.7 36.5 1.0
MG A:MG877 4.0 54.4 1.0
CG A:HIS653 4.2 25.8 1.0
CD2 A:HIS613 4.2 26.5 1.0
CG A:HIS617 4.2 22.0 1.0
CB A:ASP654 4.3 28.0 1.0
ND1 A:HIS653 4.3 26.9 1.0
ND1 A:HIS617 4.3 23.3 1.0
CB A:ASP764 4.4 27.5 1.0
O A:HOH914 4.6 28.4 1.0
OG1 A:THR621 4.6 25.5 1.0
NE2 A:HIS613 4.7 29.0 1.0
O A:ASP764 4.8 27.8 1.0
CA A:ASP764 4.9 26.5 1.0

Reference:

G.Chen, H.Wang, H.Robinson, J.Cai, Y.Wan, H.Ke. An Insight Into the Pharmacophores of Phosphodiesterase-5 Inhibitors From Synthetic and Crystal Structural Studies Biochem.Pharm. V. 75 1717 2008.
ISSN: ISSN 0006-2952
PubMed: 18346713
DOI: 10.1016/J.BCP.2008.01.019
Page generated: Thu Oct 24 11:30:48 2024

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