Magnesium in PDB 4f9a: Crystal Structure of Human Phosphodiesterase 4B with Regulatory Domain and D155988

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4B with Regulatory Domain and D155988:
3.1.4.17;

The structure of Crystal Structure of Human Phosphodiesterase 4B with Regulatory Domain and D155988, PDB code: 4f9a was solved by B.L.Staker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.63
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	95.004, 95.004, 93.714, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 23.3

The structure of Crystal Structure of Human Phosphodiesterase 4B with Regulatory Domain and D155988 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 4B with Regulatory Domain and D155988 (pdb code 4f9a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 4B with Regulatory Domain and D155988, PDB code: 4f9a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Phosphodiesterase 4B with Regulatory Domain and D155988


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Phosphodiesterase 4B with Regulatory Domain and D155988 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:22.8 occ:1.00 OD1 A:ASP447 2.3 24.8 1.0 CG A:ASP447 3.2 22.6 1.0 OD2 A:ASP447 3.5 24.9 1.0 ZN A:ZN801 3.7 29.4 1.0 CD2 A:HIS446 4.1 20.7 1.0 OG1 A:THR517 4.2 31.7 1.0 OD2 A:ASP564 4.2 30.1 1.0 O A:HOH32 4.3 28.5 1.0 O A:HIS446 4.3 22.5 1.0 OE2 A:GLU476 4.4 25.7 1.0 O A:THR517 4.4 31.6 1.0 NE2 A:HIS446 4.4 19.4 1.0 NE2 A:HIS479 4.6 19.3 1.0 CB A:ASP447 4.6 22.7 1.0 CB A:THR517 4.6 31.7 1.0 CD2 A:HIS406 4.7 27.9 1.0 CD2 A:HIS479 4.7 21.8 1.0 CD2 A:HIS450 4.8 26.4 1.0 NE2 A:HIS406 4.8 28.3 1.0 CG A:GLU476 5.0 25.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Phosphodiesterase 4B with Regulatory Domain and D155988


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Phosphodiesterase 4B with Regulatory Domain and D155988 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:14.9 occ:1.00 OD1 B:ASP447 2.2 26.3 1.0 O B:HOH92 2.3 26.1 1.0 O B:HOH98 2.5 19.0 1.0 CG B:ASP447 3.2 23.5 1.0 OD2 B:ASP447 3.5 23.9 1.0 ZN B:ZN801 3.7 31.9 1.0 OG1 B:THR517 4.2 29.0 1.0 O B:HOH4 4.2 38.2 1.0 O B:THR517 4.3 29.5 1.0 CD2 B:HIS446 4.3 21.5 1.0 OD2 B:ASP564 4.4 34.4 1.0 OE2 B:GLU476 4.4 25.4 1.0 NE2 B:HIS479 4.6 21.2 1.0 CB B:ASP447 4.6 22.8 1.0 O B:HIS446 4.6 23.1 1.0 CD2 B:HIS406 4.6 27.6 1.0 NE2 B:HIS406 4.7 26.8 1.0 NE2 B:HIS446 4.7 21.1 1.0 CD2 B:HIS450 4.7 25.4 1.0 CB B:THR517 4.8 29.7 1.0 CD2 B:HIS479 4.8 23.3 1.0

A.B.Burgin, O.T.Magnusson, J.Singh, P.Witte, B.L.Staker, J.M.Bjornsson, M.Thorsteinsdottir, S.Hrafnsdottir, T.Hagen, A.S.Kiselyov, L.J.Stewart, M.E.Gurney. Design of Phosphodiesterase 4D (PDE4D) Allosteric Modulators For Enhancing Cognition with Improved Safety. Nat.Biotechnol. V. 28 63 2010.
ISSN: ISSN 1087-0156
PubMed: 20037581
DOI: 10.1038/NBT.1598