Zinc in PDB 1xn0: Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R,S)- Rolipram

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R,S)- Rolipram:
3.1.4.17;

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R,S)- Rolipram, PDB code: 1xn0 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 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.926, 94.996, 106.833, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R,S)- Rolipram 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 (R,S)- Rolipram (pdb code 1xn0). 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 (R,S)- Rolipram, PDB code: 1xn0:
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 (R,S)- Rolipram


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 (R,S)- Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:26.9 occ:1.00 O A:HOH1009 1.9 14.7 1.0 OD2 A:ASP275 2.1 13.5 1.0 OD2 A:ASP392 2.2 11.2 1.0 NE2 A:HIS238 2.2 11.1 1.0 NE2 A:HIS274 2.2 10.8 1.0 O A:HOH1010 2.3 21.1 1.0 CG A:ASP392 3.1 15.2 1.0 CE1 A:HIS274 3.1 14.0 1.0 CD2 A:HIS238 3.2 11.5 1.0 OD1 A:ASP392 3.2 14.6 1.0 CG A:ASP275 3.2 16.9 1.0 CD2 A:HIS274 3.3 9.1 1.0 CE1 A:HIS238 3.3 15.0 1.0 MG A:MG1002 3.6 12.8 1.0 OD1 A:ASP275 3.7 18.8 1.0 O A:HOH1013 3.9 27.9 1.0 O A:HOH1008 4.0 27.1 1.0 ND1 A:HIS274 4.3 15.4 1.0 CG A:HIS238 4.3 11.1 1.0 ND1 A:HIS238 4.4 11.8 1.0 CG A:HIS274 4.4 13.4 1.0 CD2 A:HIS234 4.4 12.1 1.0 CB A:ASP275 4.4 15.6 1.0 CB A:ASP392 4.5 16.6 1.0 O A:HOH1034 4.6 27.6 1.0 NE2 A:HIS234 4.7 12.6 1.0 O A:HOH1006 4.7 20.7 1.0 CG2 A:VAL242 4.8 11.0 1.0

Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R,S)- Rolipram


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 (R,S)- Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:28.1 occ:1.00 O B:HOH2008 1.8 15.4 1.0 OD2 B:ASP392 2.1 12.1 1.0 OD2 B:ASP275 2.1 8.7 1.0 NE2 B:HIS238 2.3 13.4 1.0 NE2 B:HIS274 2.3 9.7 1.0 O B:HOH2007 2.5 24.3 1.0 CG B:ASP392 2.9 16.8 1.0 OD1 B:ASP392 3.1 16.4 1.0 CG B:ASP275 3.2 14.9 1.0 CE1 B:HIS274 3.2 16.9 1.0 CD2 B:HIS238 3.2 15.4 1.0 CE1 B:HIS238 3.2 15.0 1.0 CD2 B:HIS274 3.3 13.1 1.0 MG B:MG1002 3.7 17.5 1.0 OD1 B:ASP275 3.7 10.4 1.0 O B:HOH2006 4.0 24.3 1.0 O B:HOH2010 4.0 25.7 1.0 CD2 B:HIS234 4.3 11.4 1.0 NE2 B:HIS234 4.3 15.6 1.0 CB B:ASP392 4.3 17.1 1.0 ND1 B:HIS274 4.3 15.3 1.0 ND1 B:HIS238 4.3 11.5 1.0 CG B:HIS238 4.4 13.3 1.0 CG B:HIS274 4.4 15.4 1.0 CB B:ASP275 4.4 14.2 1.0 O B:HOH2088 4.4 35.7 1.0 O B:HOH2004 4.7 21.9 1.0 CG2 B:VAL242 4.8 16.0 1.0 CA B:ASP392 4.9 17.2 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