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

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

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- Rolipram, PDB code: 1xmy 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 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.670, 94.633, 106.432, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 29.8

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- 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)- Rolipram (pdb code 1xmy). 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)- Rolipram, PDB code: 1xmy:
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)- 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)- Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:39.1 occ:1.00 O A:HOH1007 1.8 26.9 1.0 OD2 A:ASP392 2.0 30.1 1.0 OD2 A:ASP275 2.1 29.7 1.0 NE2 A:HIS238 2.4 19.3 1.0 O A:HOH1008 2.4 18.4 1.0 NE2 A:HIS274 2.4 9.2 1.0 CG A:ASP392 3.1 26.0 1.0 CD2 A:HIS238 3.2 21.1 1.0 CG A:ASP275 3.3 25.0 1.0 CE1 A:HIS274 3.4 17.6 1.0 CD2 A:HIS274 3.4 7.6 1.0 OD1 A:ASP392 3.4 23.8 1.0 CE1 A:HIS238 3.5 20.1 1.0 MG A:MG1002 3.6 30.8 1.0 O A:HOH7 3.8 40.6 1.0 OD1 A:ASP275 3.9 19.8 1.0 O A:HOH1006 4.0 37.6 1.0 CB A:ASP275 4.3 20.8 1.0 CD2 A:HIS234 4.4 20.2 1.0 CG A:HIS238 4.5 21.1 1.0 CB A:ASP392 4.5 25.9 1.0 ND1 A:HIS274 4.5 19.0 1.0 CG A:HIS274 4.5 17.2 1.0 ND1 A:HIS238 4.6 18.3 1.0 CG2 A:VAL242 4.7 19.7 1.0 O A:HOH1004 4.7 52.0 1.0 NE2 A:HIS234 4.8 19.6 1.0 O A:HOH20 4.9 38.4 1.0

Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with (R)- 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)- Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:41.7 occ:1.00 O B:HOH2007 1.9 32.8 1.0 OD2 B:ASP392 2.1 28.7 1.0 OD2 B:ASP275 2.1 27.1 1.0 NE2 B:HIS274 2.2 12.1 1.0 O B:HOH2008 2.4 36.4 1.0 NE2 B:HIS238 2.5 23.4 1.0 CD2 B:HIS274 3.0 14.7 1.0 CG B:ASP392 3.0 25.1 1.0 CG B:ASP275 3.2 24.5 1.0 OD1 B:ASP392 3.3 24.6 1.0 CE1 B:HIS274 3.3 20.0 1.0 CD2 B:HIS238 3.4 25.8 1.0 CE1 B:HIS238 3.4 23.8 1.0 OD1 B:ASP275 3.6 21.5 1.0 MG B:MG1002 3.8 26.8 1.0 CG B:HIS274 4.2 18.1 1.0 O B:HOH12 4.3 40.0 1.0 CD2 B:HIS234 4.3 24.0 1.0 ND1 B:HIS274 4.4 16.3 1.0 CB B:ASP392 4.4 24.5 1.0 O B:HOH2006 4.4 48.1 1.0 ND1 B:HIS238 4.4 27.0 1.0 CB B:ASP275 4.4 21.7 1.0 CG B:HIS238 4.4 25.2 1.0 CG2 B:VAL242 4.5 22.0 1.0 NE2 B:HIS234 4.6 25.3 1.0 O B:HOH2004 4.6 28.0 1.0 O B:HOH33 4.7 52.2 1.0 CA B:ASP392 4.9 24.0 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