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Zinc in PDB 1xos: Catalytic Domain of Human Phosphodiesterase 4B in Complex with Sildenafil

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Sildenafil

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Sildenafil:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Sildenafil, PDB code: 1xos 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) 70.71 / 2.28
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.571, 107.117, 89.481, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.7

Other elements in 1xos:

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Sildenafil 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 4B in Complex with Sildenafil (pdb code 1xos). 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 4B in Complex with Sildenafil, PDB code: 1xos:

Zinc binding site 1 out of 1 in 1xos

Go back to Zinc Binding Sites List in 1xos
Zinc binding site 1 out of 1 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Sildenafil


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 4B in Complex with Sildenafil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:45.3
occ:1.00
 O A:HOH1007 1.9 25.5 1.0
OD2 A:ASP275 2.2 25.6 1.0
NE2 A:HIS238 2.2 30.2 1.0
OD2 A:ASP392 2.2 32.7 1.0
NE2 A:HIS274 2.2 24.8 1.0
O A:HOH1008 2.3 43.7 1.0
CG A:ASP392 3.0 36.0 1.0
CD2 A:HIS274 3.1 26.1 1.0
CD2 A:HIS238 3.1 33.0 1.0
OD1 A:ASP392 3.1 34.1 1.0
CE1 A:HIS238 3.2 31.4 1.0
CG A:ASP275 3.2 31.0 1.0
CE1 A:HIS274 3.3 33.6 1.0
OD1 A:ASP275 3.7 31.7 1.0
MG A:MG1002 3.7 30.7 1.0
O A:HOH1006 3.8 45.3 1.0
O A:HOH1009 4.0 56.5 1.0
CD2 A:HIS234 4.3 29.5 1.0
CG A:HIS238 4.3 32.5 1.0
ND1 A:HIS238 4.3 28.8 1.0
CG A:HIS274 4.3 27.4 1.0
ND1 A:HIS274 4.4 28.6 1.0
NE2 A:HIS234 4.4 31.9 1.0
CB A:ASP392 4.4 36.6 1.0
CB A:ASP275 4.4 30.2 1.0
C1 A:VIA1 4.5 90.9 1.0
O A:HOH1004 4.7 41.4 1.0
CG2 A:VAL242 4.8 34.6 1.0
CA A:ASP392 4.9 36.8 1.0
C2 A:VIA1 4.9 91.0 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 00:22:37 2025

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