Zinc in PDB 3itm: Catalytic Domain of HPDE2A

All present enzymatic activity of Catalytic Domain of HPDE2A:
3.1.4.17;

The structure of Catalytic Domain of HPDE2A, PDB code: 3itm was solved by J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.49
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.017, 108.017, 515.563, 90.00, 90.00, 120.00
R / Rfree (%)	22.7 / 28.6

The binding sites of Zinc atom in the Catalytic Domain of HPDE2A (pdb code 3itm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Catalytic Domain of HPDE2A, PDB code: 3itm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Catalytic Domain of HPDE2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of HPDE2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:33.9 occ:1.00 NE2 A:HIS660 1.9 29.3 1.0 OD2 A:ASP697 2.0 37.4 1.0 OD1 A:ASP808 2.0 45.3 1.0 NE2 A:HIS696 2.2 46.5 1.0 CE1 A:HIS660 2.8 33.6 1.0 CG A:ASP808 3.0 44.6 1.0 CD2 A:HIS660 3.0 32.7 1.0 CG A:ASP697 3.1 41.4 1.0 CE1 A:HIS696 3.2 45.2 1.0 CD2 A:HIS696 3.2 43.0 1.0 OG A:SER721 3.2 43.1 1.0 OD2 A:ASP808 3.2 50.2 1.0 OD1 A:ASP697 3.6 37.8 1.0 ND1 A:HIS660 4.0 35.2 1.0 ND1 A:HIS656 4.1 40.0 1.0 CG A:HIS660 4.1 35.4 1.0 CE1 A:HIS656 4.2 39.4 1.0 ND1 A:HIS696 4.3 45.0 1.0 CG A:HIS696 4.3 45.4 1.0 CB A:ASP808 4.3 41.3 1.0 CB A:ASP697 4.4 41.2 1.0 CB A:SER721 4.6 41.4 1.0 CG2 A:THR768 4.6 42.7 1.0 CG2 A:VAL664 4.9 41.4 1.0 CA A:ASP808 4.9 42.4 1.0

Zinc binding site 2 out of 4 in the Catalytic Domain of HPDE2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of HPDE2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:30.9 occ:1.00 NE2 B:HIS660 1.9 32.3 1.0 OD1 B:ASP808 2.0 47.1 1.0 OD2 B:ASP697 2.1 39.3 1.0 NE2 B:HIS696 2.3 44.9 1.0 CE1 B:HIS660 2.8 34.1 1.0 CG B:ASP808 2.9 45.8 1.0 CD2 B:HIS660 3.0 31.5 1.0 CD2 B:HIS696 3.1 41.3 1.0 CG B:ASP697 3.1 41.8 1.0 OD2 B:ASP808 3.2 44.9 1.0 OG B:SER721 3.3 46.5 1.0 CE1 B:HIS696 3.4 43.7 1.0 OD1 B:ASP697 3.6 39.1 1.0 ND1 B:HIS660 4.0 30.0 1.0 CD2 B:HIS656 4.0 37.2 1.0 CG B:HIS660 4.1 33.5 1.0 CB B:ASP808 4.3 42.0 1.0 CG B:HIS696 4.3 41.5 1.0 CB B:ASP697 4.4 40.8 1.0 ND1 B:HIS696 4.4 42.2 1.0 O B:HOH44 4.5 33.6 1.0 NE2 B:HIS656 4.5 39.4 1.0 CG2 B:THR768 4.5 43.2 1.0 CB B:SER721 4.7 42.4 1.0 CG2 B:VAL664 4.9 41.6 1.0 CA B:ASP808 5.0 42.4 1.0

Zinc binding site 3 out of 4 in the Catalytic Domain of HPDE2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Domain of HPDE2A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3 b:42.3 occ:1.00 NE2 C:HIS660 2.0 36.5 1.0 OD2 C:ASP697 2.1 38.7 1.0 OD1 C:ASP808 2.1 47.8 1.0 NE2 C:HIS696 2.1 44.1 1.0 CE1 C:HIS660 2.9 37.8 1.0 CG C:ASP808 2.9 45.2 1.0 CD2 C:HIS696 3.0 41.6 1.0 CD2 C:HIS660 3.1 36.9 1.0 OD2 C:ASP808 3.1 46.4 1.0 CG C:ASP697 3.1 41.4 1.0 CE1 C:HIS696 3.2 41.3 1.0 OG C:SER721 3.2 45.9 1.0 OD1 C:ASP697 3.5 40.4 1.0 ND1 C:HIS660 4.0 35.4 1.0 CG C:HIS660 4.1 36.5 1.0 ND1 C:HIS656 4.2 40.7 1.0 CG C:HIS696 4.2 40.7 1.0 CB C:ASP808 4.2 42.0 1.0 ND1 C:HIS696 4.2 37.6 1.0 O C:HOH32 4.3 31.9 1.0 CB C:ASP697 4.5 40.5 1.0 CE1 C:HIS656 4.5 41.5 1.0 CG2 C:THR768 4.5 42.6 1.0 CB C:SER721 4.7 42.2 1.0 CG2 C:VAL664 4.7 42.1 1.0 CA C:ASP808 4.8 42.7 1.0

Zinc binding site 4 out of 4 in the Catalytic Domain of HPDE2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Domain of HPDE2A within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4 b:38.8 occ:1.00 NE2 D:HIS660 2.0 37.4 1.0 OD1 D:ASP808 2.0 43.7 1.0 OD2 D:ASP697 2.1 35.3 1.0 NE2 D:HIS696 2.2 40.3 1.0 CG D:ASP808 2.8 44.0 1.0 OD2 D:ASP808 2.8 44.3 1.0 CD2 D:HIS660 2.9 36.1 1.0 CE1 D:HIS660 3.0 37.6 1.0 CD2 D:HIS696 3.0 39.9 1.0 CG D:ASP697 3.1 40.2 1.0 CE1 D:HIS696 3.3 38.7 1.0 OG D:SER721 3.4 43.1 1.0 OD1 D:ASP697 3.5 33.9 1.0 ND1 D:HIS660 4.1 37.8 1.0 CD2 D:HIS656 4.1 39.7 1.0 CG D:HIS660 4.1 37.2 1.0 CG D:HIS696 4.2 40.6 1.0 CB D:ASP808 4.2 42.7 1.0 ND1 D:HIS696 4.3 37.2 1.0 CB D:ASP697 4.5 40.5 1.0 NE2 D:HIS656 4.6 40.9 1.0 CG2 D:VAL664 4.6 43.2 1.0 CG2 D:THR768 4.6 43.4 1.0 CB D:SER721 4.8 41.7 1.0 CA D:ASP808 4.9 42.4 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