Zinc in PDB 3ibj: X-Ray Structure of PDE2A

All present enzymatic activity of X-Ray Structure of PDE2A:
3.1.4.17;

The structure of X-Ray Structure of PDE2A, PDB code: 3ibj was solved by J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.26 / 3.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.233, 89.699, 264.187, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 31.1

The structure of X-Ray Structure of PDE2A also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the X-Ray Structure of PDE2A (pdb code 3ibj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of PDE2A, PDB code: 3ibj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the X-Ray Structure of PDE2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of PDE2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:73.2 occ:1.00 OD1 A:ASP808 2.2 64.9 1.0 NE2 A:HIS660 2.2 65.1 1.0 OD2 A:ASP697 2.4 69.7 1.0 NE2 A:HIS696 2.6 67.5 1.0 CD2 A:HIS696 2.9 67.8 1.0 CE1 A:HIS660 3.0 65.0 1.0 CG A:ASP808 3.1 65.0 1.0 CD2 A:HIS660 3.3 65.4 1.0 CG A:ASP697 3.4 68.0 1.0 OD2 A:ASP808 3.5 66.7 1.0 OD1 A:ASP697 3.8 67.9 1.0 CE1 A:HIS696 3.8 67.4 1.0 MG A:MG905 4.1 58.3 1.0 CG A:HIS696 4.2 67.7 1.0 ND1 A:HIS660 4.2 65.5 1.0 CG A:HIS660 4.4 65.3 1.0 CE1 A:HIS656 4.4 74.3 1.0 CB A:ASP808 4.4 65.0 1.0 ND1 A:HIS656 4.5 74.9 1.0 ND1 A:HIS696 4.6 67.9 1.0 CA A:ASP808 4.7 64.2 1.0 CB A:ASP697 4.7 68.0 1.0 CE2 A:TYR719 4.9 84.5 1.0 CG2 A:VAL664 5.0 72.7 1.0 O A:ASP808 5.0 64.6 1.0

Zinc binding site 2 out of 2 in the X-Ray Structure of PDE2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of PDE2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:67.4 occ:1.00 NE2 B:HIS660 2.2 51.3 1.0 OD1 B:ASP808 2.5 51.6 1.0 OD2 B:ASP697 2.6 56.4 1.0 NE2 B:HIS696 2.6 54.0 1.0 CE1 B:HIS660 3.0 51.1 1.0 CD2 B:HIS696 3.0 54.2 1.0 CD2 B:HIS660 3.4 51.5 1.0 CG B:ASP808 3.4 51.7 1.0 CG B:ASP697 3.4 54.7 1.0 MG B:MG905 3.7 44.3 1.0 OD2 B:ASP808 3.7 53.4 1.0 OD1 B:ASP697 3.7 54.6 1.0 CE1 B:HIS696 3.8 53.8 1.0 ND1 B:HIS660 4.2 51.6 1.0 CG B:HIS696 4.3 54.1 1.0 CG B:HIS660 4.4 51.4 1.0 CE1 B:HIS656 4.4 61.1 1.0 ND1 B:HIS656 4.5 61.6 1.0 CE2 B:TYR719 4.6 70.9 1.0 CB B:ASP808 4.6 51.8 1.0 ND1 B:HIS696 4.7 54.4 1.0 CB B:ASP697 4.7 54.7 1.0 O B:ASP808 4.8 51.3 1.0 CA B:ASP808 4.9 51.0 1.0 CD2 B:TYR719 4.9 70.9 1.0 CG2 B:VAL664 5.0 57.8 1.0

J.Pandit, M.D.Forman, K.F.Fennell, K.S.Dillman, F.S.Menniti. Mechanism For the Allosteric Regulation of Phosphodiesterase 2A Deduced From the X-Ray Structure of A Near Full-Length Construct. Proc.Natl.Acad.Sci.Usa V. 106 18225 2009.
ISSN: ISSN 0027-8424
PubMed: 19828435
DOI: 10.1073/PNAS.0907635106