Zinc in PDB 6feb: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086:
3.1.4.53;

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086, PDB code: 6feb was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.49 / 1.93
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	95.068, 158.233, 111.405, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.6

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086 (pdb code 6feb). 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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086, PDB code: 6feb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn514 b:26.4 occ:1.00 NE2 A:HIS164 2.1 18.3 1.0 OD2 A:ASP201 2.2 20.7 1.0 NE2 A:HIS200 2.2 20.3 1.0 OD1 A:ASP318 2.2 21.1 1.0 O A:HOH621 2.3 22.0 1.0 O A:HOH693 2.4 19.2 1.0 CD2 A:HIS200 3.1 20.8 1.0 CG A:ASP318 3.1 23.3 1.0 CE1 A:HIS164 3.1 19.0 1.0 CG A:ASP201 3.1 21.6 1.0 CD2 A:HIS164 3.2 20.0 1.0 CE1 A:HIS200 3.3 20.2 1.0 OD2 A:ASP318 3.3 23.4 1.0 OD1 A:ASP201 3.6 22.9 1.0 MG A:MG513 3.9 15.4 1.0 O A:HOH728 4.0 21.5 1.0 O A:HOH670 4.1 24.2 1.0 CD2 A:HIS160 4.2 23.9 1.0 ND1 A:HIS164 4.2 19.6 1.0 CG A:HIS200 4.3 21.1 1.0 CG A:HIS164 4.3 20.0 1.0 CB A:ASP201 4.3 21.5 1.0 ND1 A:HIS200 4.3 19.4 1.0 NE2 A:HIS160 4.5 24.8 1.0 CB A:ASP318 4.5 21.9 1.0 CG2 A:VAL168 4.6 22.5 1.0 O A:HOH622 4.8 20.2 1.0 C23 A:D5Z511 5.0 26.6 1.0 CA A:ASP318 5.0 21.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn510 b:31.3 occ:1.00 OD2 B:ASP201 2.2 22.4 1.0 NE2 B:HIS164 2.2 25.3 1.0 NE2 B:HIS200 2.2 26.8 1.0 OD1 B:ASP318 2.2 26.4 1.0 O B:HOH603 2.3 23.7 1.0 O B:HOH672 2.3 26.4 1.0 CG B:ASP318 3.1 29.6 1.0 CD2 B:HIS200 3.1 22.9 1.0 CG B:ASP201 3.1 23.3 1.0 CE1 B:HIS164 3.2 24.0 1.0 CD2 B:HIS164 3.2 23.0 1.0 CE1 B:HIS200 3.3 24.4 1.0 OD2 B:ASP318 3.3 32.3 1.0 OD1 B:ASP201 3.5 24.9 1.0 MG B:MG509 3.8 19.7 1.0 O B:HOH687 4.0 24.6 1.0 O B:HOH645 4.2 27.7 1.0 CD2 B:HIS160 4.2 26.4 1.0 CG B:HIS200 4.3 22.7 1.0 ND1 B:HIS164 4.3 22.9 1.0 ND1 B:HIS200 4.3 24.4 1.0 CB B:ASP201 4.3 24.6 1.0 CG B:HIS164 4.4 25.9 1.0 NE2 B:HIS160 4.4 25.5 1.0 CB B:ASP318 4.5 30.6 1.0 CG2 B:VAL168 4.7 29.6 1.0 O B:HOH628 4.8 21.6 1.0

I.G.Salado, C.Moreno, G.Sakaine, A.K.Singh, A.R.Blaazer, M.Siderius, A.Matheeussen, S.Gul, L.Maes, R.Leurs, D.G.Brown, K.Augustyns. HPDE4D2 Structure with Inhibitor Npd-1086 To Be Published.