Magnesium 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:

Zinc

(Zn)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of PDE2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg905 b:58.3 occ:1.00 OD1 A:ASP697 2.6 67.9 1.0 OG1 A:THR768 3.4 58.3 1.0 CG A:ASP697 3.7 68.0 1.0 O A:THR768 3.7 58.3 1.0 OD2 A:ASP697 4.1 69.7 1.0 O A:HIS696 4.1 67.4 1.0 ZN A:ZN1 4.1 73.2 1.0 CB A:THR768 4.3 59.6 1.0 CD2 A:HIS696 4.5 67.8 1.0 OD2 A:ASP808 4.5 66.7 1.0 CE1 A:HIS730 4.6 59.6 1.0 O A:SER720 4.6 83.2 1.0 ND1 A:HIS730 4.6 60.1 1.0 CG A:GLU727 4.7 68.8 1.0 C A:THR768 4.7 59.3 1.0 CE1 A:HIS656 4.8 74.3 1.0 C A:HIS696 4.9 68.3 1.0 CB A:ASP697 4.9 68.0 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of PDE2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg905 b:44.3 occ:1.00 OD1 B:ASP697 2.6 54.6 1.0 CG B:ASP697 3.6 54.7 1.0 ZN B:ZN2 3.7 67.4 1.0 OD2 B:ASP697 3.8 56.4 1.0 CE1 B:HIS656 4.1 61.1 1.0 OG1 B:THR768 4.1 47.0 1.0 O B:THR768 4.2 47.0 1.0 CD2 B:HIS696 4.5 54.2 1.0 OD2 B:ASP808 4.6 53.4 1.0 ND1 B:HIS656 4.6 61.6 1.0 CE1 B:HIS730 4.7 47.0 1.0 O B:SER720 4.7 69.8 1.0 CE1 B:HIS700 4.7 65.4 1.0 O B:HIS696 4.8 53.8 1.0 CB B:THR768 4.9 48.2 1.0 N B:SER720 4.9 69.6 1.0 ND1 B:HIS700 5.0 66.0 1.0 CB B:ASP697 5.0 54.7 1.0 NE2 B:HIS656 5.0 61.2 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