Zinc in PDB 3itu: HPDE2A Catalytic Domain Complexed with Ibmx

All present enzymatic activity of HPDE2A Catalytic Domain Complexed with Ibmx:
3.1.4.17;

The structure of HPDE2A Catalytic Domain Complexed with Ibmx, PDB code: 3itu 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 / 1.58
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.815, 73.287, 91.532, 109.30, 88.80, 89.00
R / Rfree (%)	17.4 / 23.3

The structure of HPDE2A Catalytic Domain Complexed with Ibmx also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of HPDE2A Catalytic Domain Complexed with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:13.2 occ:1.00 NE2 A:HIS660 2.1 10.3 1.0 NE2 A:HIS696 2.1 7.5 1.0 OD1 A:ASP808 2.1 11.7 1.0 OD2 A:ASP697 2.1 8.2 1.0 O A:HOH922 2.3 10.6 1.0 O A:HOH6 2.4 11.2 1.0 CD2 A:HIS696 3.0 9.1 1.0 CD2 A:HIS660 3.1 8.5 1.0 CE1 A:HIS660 3.1 8.6 1.0 CG A:ASP808 3.1 10.5 1.0 CE1 A:HIS696 3.1 9.6 1.0 CG A:ASP697 3.2 6.2 1.0 OD2 A:ASP808 3.3 15.2 1.0 OD1 A:ASP697 3.7 9.8 1.0 MG A:MG920 3.9 10.5 1.0 ND1 A:HIS660 4.2 8.6 1.0 O A:HOH42 4.2 14.7 1.0 CD2 A:HIS656 4.2 9.6 1.0 CG A:HIS696 4.2 8.8 1.0 CG A:HIS660 4.2 9.8 1.0 ND1 A:HIS696 4.2 9.8 1.0 O A:HOH2 4.4 10.9 1.0 CB A:ASP697 4.4 7.2 1.0 NE2 A:HIS656 4.4 12.6 1.0 CB A:ASP808 4.4 9.4 1.0 O A:HOH4 4.7 8.7 1.0 CG2 A:VAL664 4.8 9.1 1.0 CA A:ASP808 4.8 8.2 1.0 O A:ASP808 4.9 9.3 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of HPDE2A Catalytic Domain Complexed with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:13.9 occ:1.00 OD1 B:ASP808 2.0 10.6 1.0 NE2 B:HIS696 2.1 9.6 1.0 OD2 B:ASP697 2.1 11.2 1.0 NE2 B:HIS660 2.2 10.8 1.0 O B:HOH7 2.3 13.7 1.0 O B:HOH12 2.4 14.1 1.0 CG B:ASP808 3.0 12.6 1.0 CD2 B:HIS696 3.0 11.1 1.0 CD2 B:HIS660 3.1 11.6 1.0 CE1 B:HIS696 3.1 13.4 1.0 CG B:ASP697 3.2 9.1 1.0 CE1 B:HIS660 3.2 9.8 1.0 OD2 B:ASP808 3.2 16.0 1.0 OD1 B:ASP697 3.7 9.6 1.0 MG B:MG920 3.9 10.8 1.0 O B:HOH60 4.2 18.6 1.0 CG B:HIS696 4.2 11.3 1.0 O B:HOH8 4.2 11.1 1.0 ND1 B:HIS696 4.2 9.8 1.0 ND1 B:HIS656 4.3 17.1 1.0 CG B:HIS660 4.3 12.7 1.0 ND1 B:HIS660 4.3 12.5 1.0 CE1 B:HIS656 4.3 10.5 1.0 CB B:ASP697 4.4 11.3 1.0 CB B:ASP808 4.5 12.5 1.0 O B:HOH10 4.7 10.7 1.0 CG2 B:VAL664 4.9 8.9 1.0 O B:ASP808 4.9 11.4 1.0 CA B:ASP808 4.9 10.3 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of HPDE2A Catalytic Domain Complexed with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3 b:14.4 occ:1.00 OD1 C:ASP808 2.0 11.3 1.0 NE2 C:HIS696 2.1 10.6 1.0 OD2 C:ASP697 2.1 11.2 1.0 NE2 C:HIS660 2.2 14.0 1.0 O C:HOH13 2.2 14.8 1.0 O C:HOH18 2.4 18.1 1.0 CG C:ASP808 3.0 12.4 1.0 CD2 C:HIS696 3.0 13.5 1.0 CD2 C:HIS660 3.1 14.3 1.0 CE1 C:HIS696 3.1 8.9 1.0 CG C:ASP697 3.1 7.5 1.0 CE1 C:HIS660 3.2 12.9 1.0 OD2 C:ASP808 3.3 17.8 1.0 OD1 C:ASP697 3.7 11.2 1.0 MG C:MG920 3.9 12.9 1.0 CG C:HIS696 4.2 13.7 1.0 ND1 C:HIS696 4.2 13.2 1.0 ND1 C:HIS656 4.2 14.4 1.0 CG C:HIS660 4.3 13.2 1.0 O C:HOH31 4.3 16.5 1.0 CE1 C:HIS656 4.3 10.9 1.0 O C:HOH14 4.3 11.1 1.0 ND1 C:HIS660 4.3 13.7 1.0 CB C:ASP697 4.3 10.3 1.0 CB C:ASP808 4.4 12.5 1.0 O C:HOH16 4.7 9.5 1.0 CG2 C:VAL664 4.8 11.4 1.0 CA C:ASP808 4.9 10.8 1.0 O C:ASP808 5.0 11.8 1.0

Zinc binding site 4 out of 4 in the HPDE2A Catalytic Domain Complexed with Ibmx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of HPDE2A Catalytic Domain Complexed with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4 b:14.7 occ:1.00 OD2 D:ASP697 2.0 9.2 1.0 NE2 D:HIS660 2.1 12.9 1.0 OD1 D:ASP808 2.1 11.7 1.0 NE2 D:HIS696 2.1 7.5 1.0 O D:HOH19 2.2 10.5 1.0 O D:HOH24 2.4 15.0 1.0 CD2 D:HIS696 3.0 10.6 1.0 CG D:ASP808 3.0 12.9 1.0 CD2 D:HIS660 3.1 15.5 1.0 CE1 D:HIS660 3.1 14.7 1.0 CG D:ASP697 3.1 5.4 1.0 CE1 D:HIS696 3.2 11.8 1.0 OD2 D:ASP808 3.2 17.0 1.0 OD1 D:ASP697 3.7 10.1 1.0 MG D:MG920 3.8 12.0 1.0 CD2 D:HIS656 4.2 11.4 1.0 CG D:HIS696 4.2 9.3 1.0 ND1 D:HIS660 4.2 14.3 1.0 CG D:HIS660 4.2 15.9 1.0 ND1 D:HIS696 4.2 12.8 1.0 O D:HOH20 4.2 10.2 1.0 O D:HOH113 4.3 16.7 1.0 NE2 D:HIS656 4.4 11.8 1.0 CB D:ASP697 4.4 9.1 1.0 CB D:ASP808 4.5 11.6 1.0 O D:HOH22 4.7 8.2 1.0 CG2 D:VAL664 4.9 12.4 1.0 CA D:ASP808 4.9 11.9 1.0 O D:ASP808 4.9 14.4 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