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Zinc in PDB 1xp0: Catalytic Domain of Human Phosphodiesterase 5A in Complex with Vardenafil

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Vardenafil

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Vardenafil:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Vardenafil, PDB code: 1xp0 was solved by G.L.Card, B.P.England, Y.Suzuki, D.Fong, B.Powell, B.Lee, C.Luu, M.Tabrizizad, S.Gillette, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.70 / 1.79
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 89.662, 89.662, 222.002, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 20.8

Other elements in 1xp0:

The structure of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Vardenafil also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of Human Phosphodiesterase 5A in Complex with Vardenafil (pdb code 1xp0). 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 Catalytic Domain of Human Phosphodiesterase 5A in Complex with Vardenafil, PDB code: 1xp0:

Zinc binding site 1 out of 1 in 1xp0

Go back to Zinc Binding Sites List in 1xp0
Zinc binding site 1 out of 1 in the Catalytic Domain of Human Phosphodiesterase 5A in Complex with Vardenafil


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Vardenafil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:30.1
occ:1.00
 O A:HOH1006 2.0 33.7 1.0
O A:HOH1001 2.0 27.0 1.0
NE2 A:HIS653 2.0 13.0 1.0
OD1 A:ASP764 2.1 14.6 1.0
NE2 A:HIS617 2.1 18.9 1.0
OD2 A:ASP654 2.1 13.0 1.0
CE1 A:HIS653 3.0 18.4 1.0
CG A:ASP764 3.0 16.1 1.0
CD2 A:HIS653 3.0 18.0 1.0
CD2 A:HIS617 3.1 17.5 1.0
CE1 A:HIS617 3.1 18.9 1.0
CG A:ASP654 3.1 16.5 1.0
OD2 A:ASP764 3.2 16.5 1.0
OD1 A:ASP654 3.6 16.8 1.0
MG A:MG2 3.7 24.4 1.0
O A:HOH1004 3.9 27.7 1.0
ND1 A:HIS653 4.1 15.7 1.0
CG A:HIS653 4.1 15.5 1.0
CD2 A:HIS613 4.2 21.6 1.0
ND1 A:HIS617 4.2 16.9 1.0
CG A:HIS617 4.2 17.4 1.0
CB A:ASP654 4.3 14.8 1.0
CB A:ASP764 4.4 14.6 1.0
NE2 A:HIS613 4.6 20.9 1.0
O A:HOH1002 4.7 25.6 1.0
O A:HOH1007 4.7 33.5 1.0
CA A:ASP764 4.8 14.4 1.0
O A:ASP764 4.9 14.7 1.0
OG1 A:THR621 4.9 16.4 1.0

Reference:

G.L.Card, B.P.England, Y.Suzuki, D.Fong, B.Powell, B.Lee, C.Luu, M.Tabrizizad, S.Gillette, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang. Structural Basis For the Activity of Drugs That Inhibit Phosphodiesterases. Structure V. 12 2233 2004.
ISSN: ISSN 0969-2126
PubMed: 15576036
DOI: 10.1016/J.STR.2004.10.004
Page generated: Wed Aug 20 00:23:04 2025

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