Zinc in PDB 3g58: Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq:
3.1.4.17;

The structure of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq, PDB code: 3g58 was solved by B.L.Staker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.21 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.385, 113.570, 161.129, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.3

The structure of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq (pdb code 3g58). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq, PDB code: 3g58:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn624 b:33.7 occ:1.00 O A:HOH792 2.2 25.4 1.0 NE2 A:HIS330 2.2 19.2 1.0 OD2 A:ASP367 2.2 18.2 1.0 NE2 A:HIS366 2.3 17.4 1.0 OD1 A:ASP484 2.3 21.5 1.0 CD2 A:HIS366 3.0 16.4 1.0 CD2 A:HIS330 3.1 18.6 1.0 O A:HOH729 3.1 29.3 1.0 CG A:ASP367 3.2 16.9 1.0 CG A:ASP484 3.2 21.8 1.0 CE1 A:HIS330 3.2 19.1 1.0 CE1 A:HIS366 3.4 18.9 1.0 OD2 A:ASP484 3.4 23.0 1.0 OD1 A:ASP367 3.7 18.4 1.0 MG A:MG625 3.9 22.5 1.0 O A:HOH1105 4.2 35.9 1.0 CD2 A:HIS326 4.2 18.3 1.0 CG A:HIS366 4.2 16.6 1.0 CG A:HIS330 4.3 17.8 1.0 CB A:ASP367 4.3 16.2 1.0 ND1 A:HIS330 4.3 18.1 1.0 ND1 A:HIS366 4.4 18.2 1.0 O A:HOH61 4.4 21.2 1.0 CB A:ASP484 4.5 21.6 1.0 NE2 A:HIS326 4.6 17.5 1.0 CG2 A:VAL334 4.7 17.7 1.0 O A:HOH776 5.0 19.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn624 b:34.2 occ:1.00 NE2 B:HIS330 2.1 22.8 1.0 O B:HOH876 2.2 27.9 1.0 OD2 B:ASP367 2.2 18.4 1.0 NE2 B:HIS366 2.2 20.8 1.0 OD1 B:ASP484 2.4 18.0 1.0 CD2 B:HIS366 3.0 19.5 1.0 CD2 B:HIS330 3.1 22.5 1.0 CE1 B:HIS330 3.1 22.2 1.0 CG B:ASP367 3.2 20.2 1.0 CG B:ASP484 3.2 21.6 1.0 CE1 B:HIS366 3.3 20.0 1.0 OD2 B:ASP484 3.4 21.3 1.0 O B:HOH659 3.5 40.0 1.0 OD1 B:ASP367 3.6 21.3 1.0 MG B:MG625 4.0 22.7 1.0 CD2 B:HIS326 4.2 21.2 1.0 CG B:HIS366 4.2 19.4 1.0 CG B:HIS330 4.2 22.2 1.0 ND1 B:HIS330 4.2 20.1 1.0 O B:HOH760 4.3 29.5 1.0 CB B:ASP367 4.3 19.0 1.0 ND1 B:HIS366 4.3 19.4 1.0 O B:HOH649 4.3 26.1 1.0 CB B:ASP484 4.5 21.6 1.0 CG2 B:VAL334 4.6 20.7 1.0 NE2 B:HIS326 4.6 21.4 1.0 O B:HOH639 4.9 18.2 1.0 CA B:ASP484 5.0 21.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn624 b:32.9 occ:1.00 O C:HOH1089 2.0 26.9 1.0 NE2 C:HIS330 2.2 18.7 1.0 OD2 C:ASP367 2.2 16.9 1.0 NE2 C:HIS366 2.2 18.4 1.0 OD1 C:ASP484 2.3 20.7 1.0 CD2 C:HIS366 3.0 16.5 1.0 CE1 C:HIS330 3.0 18.5 1.0 O C:HOH230 3.1 35.0 1.0 CG C:ASP484 3.1 21.2 1.0 CG C:ASP367 3.2 17.4 1.0 CD2 C:HIS330 3.2 18.1 1.0 CE1 C:HIS366 3.3 19.3 1.0 OD2 C:ASP484 3.4 21.6 1.0 OD1 C:ASP367 3.8 18.4 1.0 MG C:MG625 4.0 24.5 1.0 CG C:HIS366 4.2 16.4 1.0 CD2 C:HIS326 4.2 18.3 1.0 ND1 C:HIS330 4.2 17.2 1.0 CB C:ASP367 4.3 16.2 1.0 ND1 C:HIS366 4.3 19.0 1.0 CG C:HIS330 4.3 18.9 1.0 O C:HOH724 4.4 22.3 1.0 O C:HOH725 4.4 29.7 1.0 CB C:ASP484 4.5 21.5 1.0 CG2 C:VAL334 4.6 16.6 1.0 NE2 C:HIS326 4.7 16.6 1.0 O C:HOH635 4.9 17.3 1.0 CA C:ASP484 5.0 21.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Phosphodiesterase 4D with D155988/Pmnpq within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn624 b:32.2 occ:1.00 O D:HOH852 1.9 21.0 1.0 NE2 D:HIS330 2.1 19.9 1.0 OD2 D:ASP367 2.1 16.5 1.0 NE2 D:HIS366 2.2 17.9 1.0 OD1 D:ASP484 2.3 19.2 1.0 CD2 D:HIS366 3.0 15.9 1.0 CD2 D:HIS330 3.1 19.2 1.0 CE1 D:HIS330 3.1 18.4 1.0 CG D:ASP367 3.1 17.6 1.0 CG D:ASP484 3.2 19.6 1.0 CE1 D:HIS366 3.2 18.3 1.0 OD2 D:ASP484 3.4 21.9 1.0 O D:HOH733 3.5 35.4 1.0 OD1 D:ASP367 3.7 18.4 1.0 MG D:MG625 4.0 22.1 1.0 CG D:HIS366 4.2 15.6 1.0 CD2 D:HIS326 4.2 18.0 1.0 ND1 D:HIS330 4.2 18.0 1.0 ND1 D:HIS366 4.2 15.8 1.0 CG D:HIS330 4.3 18.3 1.0 CB D:ASP367 4.3 15.3 1.0 O D:HOH97 4.3 22.5 1.0 O D:HOH1023 4.3 21.5 1.0 CB D:ASP484 4.5 18.1 1.0 CG2 D:VAL334 4.6 14.9 1.0 NE2 D:HIS326 4.7 17.2 1.0 CA D:ASP484 5.0 18.6 1.0

A.B.Burgin, O.T.Magnusson, J.Singh, P.Witte, B.L.Staker, J.M.Bjornsson, M.Thorsteinsdottir, S.Hrafnsdottir, T.Hagen, A.S.Kiselyov, L.J.Stewart, M.E.Gurney. Design of Phosphodiesterase 4D (PDE4D) Allosteric Modulators For Enhancing Cognition with Improved Safety. Nat.Biotechnol. V. 28 63 2010.
ISSN: ISSN 1087-0156
PubMed: 20037581
DOI: 10.1038/NBT.1598