Zinc in PDB 1xot: Catalytic Domain of Human Phosphodiesterase 4B in Complex with Vardenafil

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

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Vardenafil, PDB code: 1xot 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 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.841, 94.423, 108.755, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.9

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Vardenafil also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Vardenafil (pdb code 1xot). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Vardenafil, PDB code: 1xot:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B 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 4B in Complex with Vardenafil within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:44.5 occ:1.00 O B:HOH2007 2.0 45.6 1.0 NE2 B:HIS274 2.1 25.2 1.0 O B:HOH2008 2.1 45.5 1.0 OD2 B:ASP392 2.2 33.8 1.0 OD2 B:ASP275 2.3 26.6 1.0 NE2 B:HIS238 2.3 16.5 1.0 CE1 B:HIS274 3.0 21.8 1.0 CD2 B:HIS274 3.0 20.5 1.0 CG B:ASP392 3.1 25.8 1.0 OD1 B:ASP392 3.2 28.8 1.0 CD2 B:HIS238 3.3 19.3 1.0 CG B:ASP275 3.3 24.2 1.0 CE1 B:HIS238 3.3 16.3 1.0 OD1 B:ASP275 3.7 24.7 1.0 MG B:MG1002 3.8 30.6 1.0 ND1 B:HIS274 4.1 21.0 1.0 O B:HOH2 4.1 39.7 1.0 CG B:HIS274 4.1 21.2 1.0 C1 B:VDN102 4.3 65.1 0.8 CG B:HIS238 4.4 20.9 1.0 ND1 B:HIS238 4.4 19.4 1.0 CB B:ASP275 4.5 22.5 1.0 CB B:ASP392 4.5 25.2 1.0 O B:HOH2006 4.5 39.6 1.0 O B:HOH2004 4.5 35.1 1.0 CG2 B:VAL242 4.6 17.4 1.0 CD2 B:HIS234 4.6 25.8 1.0 NE2 B:HIS234 4.9 22.1 1.0 CA B:ASP392 5.0 25.2 1.0

Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Vardenafil


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Vardenafil within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:46.3 occ:1.00 O A:HOH1008 1.8 59.5 1.0 OD2 A:ASP392 1.9 27.4 1.0 O A:HOH1007 2.1 37.9 1.0 NE2 A:HIS274 2.3 17.4 1.0 OD2 A:ASP275 2.3 22.3 1.0 NE2 A:HIS238 2.4 31.8 1.0 CG A:ASP392 3.0 28.2 1.0 CD2 A:HIS274 3.1 20.0 1.0 CG A:ASP275 3.2 22.2 1.0 CE1 A:HIS274 3.3 25.8 1.0 CD2 A:HIS238 3.3 30.3 1.0 OD1 A:ASP392 3.4 33.9 1.0 CE1 A:HIS238 3.4 32.9 1.0 OD1 A:ASP275 3.5 22.2 1.0 MG A:MG1002 3.8 35.3 1.0 O A:HOH1006 4.2 40.2 1.0 CG A:HIS274 4.3 21.7 1.0 ND1 A:HIS274 4.3 20.2 1.0 CB A:ASP392 4.3 27.4 1.0 CD2 A:HIS234 4.4 19.6 1.0 C1 A:VDN101 4.4 64.1 0.8 CB A:ASP275 4.4 20.4 1.0 CG A:HIS238 4.5 29.1 1.0 ND1 A:HIS238 4.5 31.4 1.0 O A:HOH1004 4.6 33.1 1.0 NE2 A:HIS234 4.6 25.2 1.0 CG2 A:VAL242 4.7 25.2 1.0 CA A:ASP392 4.9 27.1 1.0 O A:HOH1005 5.0 43.4 1.0

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