Zinc in PDB 1f0j: Catalytic Domain of Human Phosphodiesterase 4B2B

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B2B:
3.1.4.17;

The structure of Catalytic Domain of Human Phosphodiesterase 4B2B, PDB code: 1f0j was solved by R.X.Xu, A.M.Hassell, D.Vanderwall, M.H.Lambert, W.D.Holmes, M.A.Luther, W.J.Rocque, M.V.Milburn, Y.Zhao, H.Ke, R.T.Nolte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.00 / 1.77
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	104.540, 159.580, 109.040, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 22.3

The structure of Catalytic Domain of Human Phosphodiesterase 4B2B also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Arsenic	(As)	5 atoms

The binding sites of Zinc atom in the Catalytic Domain of Human Phosphodiesterase 4B2B (pdb code 1f0j). 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 4B2B, PDB code: 1f0j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B2B


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 4B2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:21.5 occ:1.00 O A:HOH1624 1.9 25.5 1.0 NE2 A:HIS238 2.0 13.8 1.0 NE2 A:HIS274 2.0 13.2 1.0 OD1 A:ASP392 2.2 18.4 1.0 OD2 A:ASP275 2.3 13.7 1.0 CD2 A:HIS274 3.0 12.9 1.0 CD2 A:HIS238 3.0 13.6 1.0 CG A:ASP392 3.0 19.0 1.0 CE1 A:HIS238 3.0 13.1 1.0 CE1 A:HIS274 3.0 13.7 1.0 OD2 A:ASP392 3.3 19.8 1.0 CG A:ASP275 3.4 13.3 1.0 AS A:ARS1103 3.6 40.5 1.0 OD1 A:ASP275 4.0 13.5 1.0 MG A:MG1102 4.0 52.3 1.0 ND1 A:HIS238 4.2 13.8 1.0 CG A:HIS274 4.2 13.6 1.0 ND1 A:HIS274 4.2 13.1 1.0 CG A:HIS238 4.2 13.9 1.0 CD2 A:HIS234 4.2 16.8 1.0 O A:HOH1330 4.3 28.8 1.0 CB A:ASP392 4.4 18.7 1.0 CG2 A:VAL242 4.5 16.4 1.0 CB A:ASP275 4.5 13.0 1.0 NE2 A:HIS234 4.5 17.4 1.0 CA A:ASP392 4.9 18.6 1.0

Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B2B


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 4B2B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:22.1 occ:1.00 O B:HOH1541 1.9 29.3 1.0 NE2 B:HIS238 2.0 17.3 1.0 NE2 B:HIS274 2.0 15.3 1.0 OD1 B:ASP392 2.2 18.2 1.0 OD2 B:ASP275 2.3 14.6 1.0 CD2 B:HIS274 3.0 15.2 1.0 CD2 B:HIS238 3.0 17.1 1.0 CE1 B:HIS238 3.0 17.0 1.0 CE1 B:HIS274 3.0 15.7 1.0 CG B:ASP392 3.1 19.1 1.0 CG B:ASP275 3.3 14.8 1.0 OD2 B:ASP392 3.3 19.6 1.0 AS B:ARS1203 3.7 43.3 1.0 OD1 B:ASP275 3.8 15.0 1.0 MG B:MG1202 4.1 45.9 1.0 ND1 B:HIS274 4.2 15.1 1.0 CG B:HIS274 4.2 15.2 1.0 ND1 B:HIS238 4.2 17.5 1.0 CG B:HIS238 4.2 17.5 1.0 O B:HOH1250 4.3 25.1 1.0 CD2 B:HIS234 4.3 18.9 1.0 CB B:ASP392 4.4 19.0 1.0 CB B:ASP275 4.4 14.5 1.0 CG2 B:VAL242 4.5 18.3 1.0 O B:HOH1543 4.7 34.7 1.0 NE2 B:HIS234 4.7 18.7 1.0 CA B:ASP392 4.9 19.4 1.0

R.X.Xu, A.M.Hassell, D.Vanderwall, M.H.Lambert, W.D.Holmes, M.A.Luther, W.J.Rocque, M.V.Milburn, Y.Zhao, H.Ke, R.T.Nolte. Atomic Structure of PDE4: Insights Into Phosphodiesterase Mechanism and Specificity. Science V. 288 1822 2000.
ISSN: ISSN 0036-8075
PubMed: 10846163
DOI: 10.1126/SCIENCE.288.5472.1822