Zinc in PDB 1zkn: Structure of PDE4D2-Ibmx

All present enzymatic activity of Structure of PDE4D2-Ibmx:
3.1.4.17;

The structure of Structure of PDE4D2-Ibmx, PDB code: 1zkn was solved by Q.Huai, Y.Liu, S.H.Francis, J.D.Corbin, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.704, 111.703, 159.387, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 26

The structure of Structure of PDE4D2-Ibmx also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Structure of PDE4D2-Ibmx (pdb code 1zkn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of PDE4D2-Ibmx, PDB code: 1zkn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of PDE4D2-Ibmx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of PDE4D2-Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:25.0 occ:1.00 OD2 A:ASP201 2.1 19.9 1.0 OD1 A:ASP318 2.1 24.4 1.0 NE2 A:HIS164 2.1 19.2 1.0 NE2 A:HIS200 2.1 22.6 1.0 O A:HOH621 2.4 29.3 1.0 CD2 A:HIS200 2.9 20.4 1.0 CG A:ASP318 3.0 24.0 1.0 CD2 A:HIS164 3.1 17.6 1.0 CE1 A:HIS164 3.1 17.4 1.0 CG A:ASP201 3.2 17.1 1.0 CE1 A:HIS200 3.2 22.0 1.0 OD2 A:ASP318 3.3 26.0 1.0 OD1 A:ASP201 3.7 17.0 1.0 MG A:MG602 4.0 30.4 1.0 CG A:HIS200 4.1 20.3 1.0 CD2 A:HIS160 4.2 15.0 1.0 ND1 A:HIS164 4.2 17.3 1.0 CG A:HIS164 4.2 17.8 1.0 ND1 A:HIS200 4.2 21.2 1.0 O A:HOH636 4.3 36.9 1.0 CB A:ASP201 4.3 17.8 1.0 CB A:ASP318 4.3 23.6 1.0 CG2 A:VAL168 4.6 19.5 1.0 NE2 A:HIS160 4.6 14.7 1.0 CA A:ASP318 4.9 23.3 1.0

Zinc binding site 2 out of 4 in the Structure of PDE4D2-Ibmx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of PDE4D2-Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:27.9 occ:1.00 OD2 B:ASP201 2.1 24.9 1.0 OD1 B:ASP318 2.1 26.3 1.0 NE2 B:HIS200 2.1 22.6 1.0 NE2 B:HIS164 2.1 21.3 1.0 O B:HOH624 2.4 34.5 1.0 CG B:ASP318 3.0 25.9 1.0 CD2 B:HIS200 3.0 21.8 1.0 CD2 B:HIS164 3.0 20.9 1.0 CG B:ASP201 3.1 23.5 1.0 CE1 B:HIS200 3.1 23.2 1.0 CE1 B:HIS164 3.2 19.5 1.0 OD2 B:ASP318 3.3 27.6 1.0 OD1 B:ASP201 3.5 23.8 1.0 MG B:MG602 3.9 44.7 1.0 O B:HOH620 4.2 29.8 1.0 CG B:HIS200 4.2 21.5 1.0 ND1 B:HIS200 4.2 22.1 1.0 CG B:HIS164 4.2 21.3 1.0 ND1 B:HIS164 4.2 20.2 1.0 CD2 B:HIS160 4.2 20.8 1.0 CB B:ASP201 4.3 23.5 1.0 CB B:ASP318 4.4 25.5 1.0 CG2 B:VAL168 4.6 26.2 1.0 NE2 B:HIS160 4.7 18.5 1.0 O B:HOH606 4.9 24.7 1.0 CA B:ASP318 5.0 24.6 1.0

Zinc binding site 3 out of 4 in the Structure of PDE4D2-Ibmx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of PDE4D2-Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:28.4 occ:1.00 OD2 C:ASP201 2.1 22.3 1.0 OD1 C:ASP318 2.1 28.1 1.0 NE2 C:HIS164 2.1 23.2 1.0 NE2 C:HIS200 2.1 23.4 1.0 CD2 C:HIS200 2.9 21.1 1.0 CG C:ASP318 3.1 28.5 1.0 CE1 C:HIS164 3.1 21.7 1.0 CD2 C:HIS164 3.1 22.2 1.0 CG C:ASP201 3.1 21.3 1.0 CE1 C:HIS200 3.2 22.9 1.0 OD2 C:ASP318 3.4 30.1 1.0 OD1 C:ASP201 3.7 21.2 1.0 MG C:MG602 3.9 35.2 1.0 CG C:HIS200 4.1 21.6 1.0 ND1 C:HIS164 4.2 23.5 1.0 CG C:HIS164 4.2 21.9 1.0 ND1 C:HIS200 4.2 21.7 1.0 CD2 C:HIS160 4.3 22.0 1.0 CB C:ASP201 4.3 21.1 1.0 O C:HOH620 4.3 33.3 1.0 CB C:ASP318 4.4 28.6 1.0 CG2 C:VAL168 4.5 21.6 1.0 NE2 C:HIS160 4.7 21.8 1.0 CA C:ASP318 5.0 28.7 1.0 O C:HOH621 5.0 25.1 1.0

Zinc binding site 4 out of 4 in the Structure of PDE4D2-Ibmx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of PDE4D2-Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:25.4 occ:1.00 OD2 D:ASP201 2.1 22.3 1.0 OD1 D:ASP318 2.1 23.1 1.0 NE2 D:HIS200 2.1 19.5 1.0 NE2 D:HIS164 2.1 19.8 1.0 O D:HOH639 2.3 23.6 1.0 CG D:ASP318 3.0 23.1 1.0 CD2 D:HIS200 3.1 17.5 1.0 CD2 D:HIS164 3.1 19.5 1.0 CE1 D:HIS200 3.1 18.9 1.0 CE1 D:HIS164 3.1 19.8 1.0 CG D:ASP201 3.1 21.1 1.0 OD2 D:ASP318 3.3 24.8 1.0 OD1 D:ASP201 3.7 22.8 1.0 MG D:MG602 4.0 29.1 1.0 ND1 D:HIS200 4.2 18.7 1.0 CG D:HIS200 4.2 18.9 1.0 CD2 D:HIS160 4.2 23.4 1.0 ND1 D:HIS164 4.2 17.7 1.0 CG D:HIS164 4.2 18.1 1.0 CB D:ASP201 4.3 20.9 1.0 CB D:ASP318 4.4 22.9 1.0 CG2 D:VAL168 4.6 16.5 1.0 NE2 D:HIS160 4.6 25.1 1.0 CA D:ASP318 5.0 21.7 1.0

Q.Huai, Y.Liu, S.H.Francis, J.D.Corbin, H.Ke. Crystal Structures of Phosphodiesterases 4 and 5 in Complex with Inhibitor 3-Isobutyl-1-Methylxanthine Suggest A Conformation Determinant of Inhibitor Selectivity J.Biol.Chem. V. 279 13095 2004.
ISSN: ISSN 0021-9258
PubMed: 14668322
DOI: 10.1074/JBC.M311556200