Zinc in PDB 1xor: Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine

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

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine, PDB code: 1xor 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)	81.65 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.279, 78.401, 163.471, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.5

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

Fluorine	(F)	12 atoms
Magnesium	(Mg)	2 atoms

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

Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine


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 4D in Complex with Zardaverine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:14.4 occ:1.00 OD2 A:ASP201 2.1 9.9 1.0 O A:HOH1007 2.1 13.6 1.0 O1 A:ZAR701 2.1 13.9 0.4 OD1 A:ASP318 2.1 8.8 1.0 O1 A:ZAR701 2.2 8.7 0.5 NE2 A:HIS164 2.2 9.0 1.0 NE2 A:HIS200 2.2 8.5 1.0 CD2 A:HIS200 3.1 8.6 1.0 CG A:ASP318 3.1 9.8 1.0 CG A:ASP201 3.1 9.1 1.0 CE1 A:HIS164 3.2 9.0 1.0 CD2 A:HIS164 3.2 8.6 1.0 C2 A:ZAR701 3.2 14.8 0.5 CE1 A:HIS200 3.3 9.2 1.0 C2 A:ZAR701 3.3 17.0 0.4 OD2 A:ASP318 3.3 15.1 1.0 OD1 A:ASP201 3.6 8.7 1.0 MG A:MG1002 3.7 9.2 1.0 C7 A:ZAR701 3.8 14.6 0.5 O A:HOH1006 3.9 13.6 1.0 N3 A:ZAR701 3.9 15.9 0.4 CG A:HIS200 4.3 9.3 1.0 ND1 A:HIS164 4.3 8.8 1.0 CB A:ASP201 4.3 8.7 1.0 CG A:HIS164 4.3 8.6 1.0 ND1 A:HIS200 4.3 9.3 1.0 CD2 A:HIS160 4.3 10.4 1.0 N3 A:ZAR701 4.4 14.7 0.5 C7 A:ZAR701 4.4 17.1 0.4 CB A:ASP318 4.5 9.5 1.0 O A:HOH1158 4.5 36.0 1.0 CG2 A:VAL168 4.8 10.0 1.0 O A:HOH1004 4.8 11.3 1.0 NE2 A:HIS160 4.8 11.3 1.0 CA A:ASP318 4.9 9.3 1.0

Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine


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 4D in Complex with Zardaverine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:15.7 occ:1.00 OD2 B:ASP201 2.1 9.2 1.0 O1 B:ZAR704 2.1 17.9 0.3 O B:HOH2007 2.1 13.9 1.0 OD1 B:ASP318 2.2 9.8 1.0 O1 B:ZAR704 2.2 9.5 0.5 NE2 B:HIS164 2.2 7.8 1.0 NE2 B:HIS200 2.2 8.2 1.0 CD2 B:HIS200 3.1 9.2 1.0 CG B:ASP318 3.1 10.8 1.0 CG B:ASP201 3.1 8.7 1.0 CD2 B:HIS164 3.1 7.5 1.0 CE1 B:HIS164 3.2 8.3 1.0 C2 B:ZAR704 3.2 15.5 0.5 C2 B:ZAR704 3.3 19.4 0.3 CE1 B:HIS200 3.3 8.8 1.0 OD2 B:ASP318 3.3 15.4 1.0 OD1 B:ASP201 3.6 8.8 1.0 MG B:MG1002 3.7 10.1 1.0 C7 B:ZAR704 3.8 16.4 0.5 O B:HOH2006 3.9 14.7 1.0 N3 B:ZAR704 4.0 18.9 0.3 CG B:HIS200 4.2 8.9 1.0 ND1 B:HIS164 4.3 8.9 1.0 CG B:HIS164 4.3 8.2 1.0 CB B:ASP201 4.3 8.5 1.0 CD2 B:HIS160 4.3 9.4 1.0 ND1 B:HIS200 4.3 8.5 1.0 C7 B:ZAR704 4.4 19.7 0.3 N3 B:ZAR704 4.4 16.6 0.5 CB B:ASP318 4.5 9.5 1.0 O B:HOH2173 4.5 35.3 1.0 CG2 B:VAL168 4.7 9.7 1.0 NE2 B:HIS160 4.7 10.5 1.0 O B:HOH2004 4.8 12.6 1.0 CA B:ASP318 5.0 9.5 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