Zinc in PDB 2yy2: Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx

All present enzymatic activity of Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx:
3.1.4.35;

The structure of Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx, PDB code: 2yy2 was solved by N.Handa, M.Shirouzu, T.Terada, K.Omori, J.Kotera, S.Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.95 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.270, 104.270, 269.610, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24

The structure of Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx (pdb code 2yy2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx, PDB code: 2yy2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Human Phosphodiesterase 9A 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 Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:55.6 occ:1.00 OD2 A:ASP293 2.2 29.0 1.0 OD1 A:ASP402 2.3 28.7 1.0 NE2 A:HIS292 2.3 28.1 1.0 NE2 A:HIS256 2.5 33.2 1.0 CG A:ASP293 3.1 28.3 1.0 CG A:ASP402 3.1 27.9 1.0 CD2 A:HIS292 3.2 27.9 1.0 OD2 A:ASP402 3.2 28.0 1.0 OD1 A:ASP293 3.4 30.8 1.0 CE1 A:HIS292 3.4 29.0 1.0 CE1 A:HIS256 3.4 33.2 1.0 CD2 A:HIS256 3.4 33.6 1.0 MG A:MG1102 3.9 30.6 1.0 CD2 A:HIS252 4.1 29.9 1.0 CG A:HIS292 4.4 27.2 1.0 NE2 A:HIS252 4.4 31.4 1.0 ND1 A:HIS292 4.4 29.6 1.0 CB A:ASP293 4.4 25.3 1.0 ND1 A:HIS256 4.5 33.8 1.0 CB A:ASP402 4.5 30.2 1.0 CG A:HIS256 4.6 34.0 1.0 O A:ASP402 4.6 33.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Human Phosphodiesterase 9A 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 Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:59.9 occ:1.00 OD2 B:ASP293 2.2 36.4 1.0 OD1 B:ASP402 2.2 36.5 1.0 NE2 B:HIS292 2.4 32.1 1.0 NE2 B:HIS256 2.6 39.4 1.0 CD2 B:HIS292 3.1 32.3 1.0 CG B:ASP402 3.2 38.2 1.0 CG B:ASP293 3.2 33.7 1.0 O B:HOH1109 3.2 21.1 1.0 OD2 B:ASP402 3.4 39.3 1.0 OD1 B:ASP293 3.5 35.7 1.0 CD2 B:HIS256 3.5 38.6 1.0 CE1 B:HIS292 3.5 32.9 1.0 CE1 B:HIS256 3.6 39.2 1.0 MG B:MG1104 3.7 26.3 1.0 CD2 B:HIS252 3.9 36.2 1.0 NE2 B:HIS252 4.2 38.0 1.0 CG B:HIS292 4.3 31.5 1.0 O B:ASP402 4.5 36.9 1.0 CB B:ASP293 4.5 31.5 1.0 ND1 B:HIS292 4.5 31.8 1.0 CB B:ASP402 4.6 37.1 1.0 CG B:HIS256 4.7 38.1 1.0 ND1 B:HIS256 4.7 37.3 1.0

N.Handa, M.Shirouzu, T.Terada, K.Omori, J.Kotera, S.Yokoyama. Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain To Be Published.