Magnesium 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:

Zinc

(Zn)

4 atoms

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of HPDE2A Catalytic Domain Complexed with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg920 b:10.5 occ:1.00 O A:HOH922 2.0 10.6 1.0 OD1 A:ASP697 2.1 9.8 1.0 O A:HOH4 2.1 8.7 1.0 O A:HOH2 2.1 10.9 1.0 O A:HOH3 2.1 11.0 1.0 O A:HOH5 2.2 9.8 1.0 CG A:ASP697 3.1 6.2 1.0 OD2 A:ASP697 3.4 8.2 1.0 O A:HOH226 3.8 22.4 1.0 ZN A:ZN1 3.9 13.2 1.0 CE1 A:HIS730 4.1 8.0 1.0 O A:HOH6 4.1 11.2 1.0 OE2 A:GLU727 4.1 12.7 1.0 OG1 A:THR768 4.2 9.0 1.0 CD2 A:HIS696 4.2 9.1 1.0 O A:HOH143 4.3 14.1 1.0 O A:HIS696 4.3 10.4 1.0 ND1 A:HIS730 4.3 11.5 1.0 CB A:ASP697 4.5 7.2 1.0 OD2 A:ASP808 4.5 15.2 1.0 NE2 A:HIS656 4.5 12.6 1.0 CB A:THR768 4.6 8.1 1.0 ND1 A:HIS700 4.6 15.0 1.0 O A:HOH484 4.6 26.2 1.0 CD2 A:HIS656 4.6 9.6 1.0 O A:THR768 4.7 11.6 1.0 NE2 A:HIS696 4.7 7.5 1.0 CE1 A:HIS700 4.7 8.3 1.0 CA A:ASP697 4.8 7.3 1.0 CG A:GLU727 4.9 10.1 1.0 CD A:GLU727 4.9 11.3 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of HPDE2A Catalytic Domain Complexed with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg920 b:10.8 occ:1.00 O B:HOH9 2.0 11.2 1.0 OD1 B:ASP697 2.0 9.6 1.0 O B:HOH10 2.1 10.7 1.0 O B:HOH11 2.1 11.6 1.0 O B:HOH7 2.1 13.7 1.0 O B:HOH8 2.1 11.1 1.0 CG B:ASP697 3.0 9.1 1.0 OD2 B:ASP697 3.4 11.2 1.0 O B:HOH464 3.9 26.2 1.0 ZN B:ZN2 3.9 13.9 1.0 NE2 B:HIS730 4.1 9.6 1.0 O B:HOH12 4.1 14.1 1.0 OE2 B:GLU727 4.1 15.5 1.0 OG1 B:THR768 4.2 10.4 1.0 O B:HIS696 4.2 10.9 1.0 CD2 B:HIS696 4.2 11.1 1.0 CD2 B:HIS730 4.3 8.5 1.0 O B:HOH46 4.3 15.3 1.0 CB B:ASP697 4.4 11.3 1.0 O B:HOH1037 4.4 27.1 1.0 CD2 B:HIS700 4.5 13.3 1.0 CE1 B:HIS656 4.5 10.5 1.0 OD2 B:ASP808 4.5 16.0 1.0 NE2 B:HIS696 4.6 9.6 1.0 CB B:THR768 4.6 11.8 1.0 O B:THR768 4.7 11.9 1.0 CA B:ASP697 4.7 11.3 1.0 ND1 B:HIS656 4.7 17.1 1.0 NE2 B:HIS700 4.9 13.5 1.0 CG B:GLU727 4.9 10.1 1.0 CD B:GLU727 4.9 11.0 1.0 C B:HIS696 5.0 10.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of HPDE2A Catalytic Domain Complexed with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg920 b:12.9 occ:1.00 O C:HOH14 2.0 11.1 1.0 O C:HOH15 2.0 12.2 1.0 O C:HOH16 2.1 9.5 1.0 OD1 C:ASP697 2.1 11.2 1.0 O C:HOH13 2.1 14.8 1.0 O C:HOH17 2.1 11.8 1.0 CG C:ASP697 3.1 7.5 1.0 OD2 C:ASP697 3.5 11.2 1.0 O C:HOH390 3.8 29.8 1.0 ZN C:ZN3 3.9 14.4 1.0 CE1 C:HIS730 4.0 9.4 1.0 O C:HOH18 4.1 18.1 1.0 OE2 C:GLU727 4.1 14.7 1.0 OG1 C:THR768 4.2 10.2 1.0 CD2 C:HIS696 4.2 13.5 1.0 O C:HOH118 4.2 16.6 1.0 O C:HIS696 4.3 12.1 1.0 ND1 C:HIS730 4.4 14.0 1.0 CE1 C:HIS656 4.4 10.9 1.0 CD2 C:HIS700 4.5 13.9 1.0 CB C:ASP697 4.5 10.3 1.0 O C:THR768 4.5 12.0 1.0 OD2 C:ASP808 4.6 17.8 1.0 CB C:THR768 4.6 11.8 1.0 ND1 C:HIS656 4.6 14.4 1.0 NE2 C:HIS696 4.6 10.6 1.0 NE2 C:HIS700 4.7 12.7 1.0 CA C:ASP697 4.8 10.0 1.0 O C:HOH978 4.8 28.8 1.0 CG C:GLU727 4.9 12.7 1.0 CD C:GLU727 5.0 13.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of HPDE2A Catalytic Domain Complexed with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg920 b:12.0 occ:1.00 O D:HOH19 2.0 10.5 1.0 OD1 D:ASP697 2.1 10.1 1.0 O D:HOH20 2.1 10.2 1.0 O D:HOH21 2.1 10.2 1.0 O D:HOH22 2.1 8.2 1.0 O D:HOH23 2.2 10.7 1.0 CG D:ASP697 3.1 5.4 1.0 OD2 D:ASP697 3.4 9.2 1.0 O D:HOH984 3.8 28.5 1.0 ZN D:ZN4 3.8 14.7 1.0 NE2 D:HIS730 4.0 9.7 1.0 O D:HOH24 4.0 15.0 1.0 OE2 D:GLU727 4.1 16.0 1.0 OG1 D:THR768 4.2 9.0 1.0 O D:HOH104 4.2 13.8 1.0 CD2 D:HIS696 4.2 10.6 1.0 O D:HIS696 4.3 10.8 1.0 CD2 D:HIS730 4.4 7.1 1.0 OD2 D:ASP808 4.4 17.0 1.0 CD2 D:HIS700 4.5 11.8 1.0 CB D:THR768 4.5 9.2 1.0 CB D:ASP697 4.5 9.1 1.0 NE2 D:HIS656 4.5 11.8 1.0 O D:THR768 4.6 12.5 1.0 CD2 D:HIS656 4.6 11.4 1.0 NE2 D:HIS700 4.7 13.8 1.0 NE2 D:HIS696 4.7 7.5 1.0 O D:HOH220 4.8 21.8 1.0 CA D:ASP697 4.8 8.3 1.0 CG D:GLU727 4.9 10.2 1.0 CD D:GLU727 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