Zinc in PDB 3ecm: Crystal Structure of the Unliganded PDE8A Catalytic Domain

All present enzymatic activity of Crystal Structure of the Unliganded PDE8A Catalytic Domain:
3.1.4.17;

The structure of Crystal Structure of the Unliganded PDE8A Catalytic Domain, PDB code: 3ecm was solved by H.Wang, Z.Yan, S.Yang, J.Cai, H.Robinson, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	76.261, 132.661, 101.517, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 26.5

The structure of Crystal Structure of the Unliganded PDE8A Catalytic Domain also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Unliganded PDE8A Catalytic Domain (pdb code 3ecm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Unliganded PDE8A Catalytic Domain, PDB code: 3ecm:

Zinc binding site 1 out of 1 in the Crystal Structure of the Unliganded PDE8A Catalytic Domain


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 the Unliganded PDE8A Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:34.9 occ:1.00 OD1 A:ASP726 2.2 27.1 1.0 OD2 A:ASP597 2.2 31.3 1.0 NE2 A:HIS560 2.3 26.5 1.0 O A:HOH820 2.3 28.3 1.0 NE2 A:HIS596 2.4 29.8 1.0 O A:HOH821 2.4 31.7 1.0 CD2 A:HIS596 3.1 30.8 1.0 CG A:ASP726 3.1 33.2 1.0 CD2 A:HIS560 3.1 28.5 1.0 CG A:ASP597 3.2 32.8 1.0 CE1 A:HIS560 3.3 27.9 1.0 OD2 A:ASP726 3.4 31.0 1.0 CE1 A:HIS596 3.5 33.1 1.0 OD1 A:ASP597 3.8 31.0 1.0 O A:HOH822 3.9 33.5 1.0 MG A:MG2 4.0 36.2 1.0 O A:HOH827 4.0 36.4 1.0 CG A:HIS596 4.3 32.7 1.0 CG A:HIS560 4.3 27.6 1.0 CB A:ASP597 4.3 29.2 1.0 CD2 A:HIS556 4.4 26.3 1.0 ND1 A:HIS560 4.4 28.5 1.0 NE2 A:HIS556 4.4 28.9 1.0 CB A:ASP726 4.5 28.7 1.0 ND1 A:HIS596 4.5 32.8 1.0 CG2 A:VAL564 4.6 26.6 1.0 O A:ASP726 4.7 31.6 1.0 CA A:ASP726 4.9 29.9 1.0 O A:HOH823 4.9 31.6 1.0

H.Wang, Z.Yan, S.Yang, J.Cai, H.Robinson, H.Ke. Kinetic and Structural Studies of Phosphodiesterase-8A and Implication on the Inhibitor Selectivity Biochemistry V. 47 12760 2008.
ISSN: ISSN 0006-2960
PubMed: 18983167
DOI: 10.1021/BI801487X