Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1086, PDB code: 6feb:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg513 b:15.4 occ:1.00 O A:HOH648 2.1 20.7 1.0 OD1 A:ASP201 2.1 22.9 1.0 O A:HOH621 2.1 22.0 1.0 O A:HOH728 2.1 21.5 1.0 O A:HOH622 2.1 20.2 1.0 O A:HOH665 2.1 18.7 1.0 CG A:ASP201 3.1 21.6 1.0 OD2 A:ASP201 3.5 20.7 1.0 ZN A:ZN514 3.9 26.4 1.0 OE2 A:GLU230 3.9 24.6 1.0 O A:HOH708 4.1 25.2 1.0 NE2 A:HIS233 4.1 18.2 1.0 O A:HIS200 4.2 20.6 1.0 CD2 A:HIS200 4.2 20.8 1.0 O A:HOH693 4.2 19.2 1.0 OG1 A:THR271 4.2 23.5 1.0 CD2 A:HIS233 4.3 17.7 1.0 CB A:ASP201 4.5 21.5 1.0 C23 A:D5Z511 4.5 26.6 1.0 OD2 A:ASP318 4.5 23.4 1.0 CD2 A:HIS204 4.5 23.3 1.0 O A:THR271 4.6 22.7 1.0 NE2 A:HIS200 4.6 20.3 1.0 C22 A:D5Z511 4.7 27.4 1.0 CG A:GLU230 4.7 22.1 1.0 O A:HOH650 4.7 30.2 1.0 NE2 A:HIS204 4.7 21.8 1.0 CB A:THR271 4.7 26.0 1.0 CD A:GLU230 4.8 27.1 1.0 CA A:ASP201 4.8 20.5 1.0 NE2 A:HIS160 4.9 24.8 1.0 CD2 A:HIS160 4.9 23.9 1.0 C A:HIS200 5.0 21.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg509 b:19.7 occ:1.00 O B:HOH628 2.1 21.6 1.0 O B:HOH603 2.1 23.7 1.0 OD1 B:ASP201 2.1 24.9 1.0 O B:HOH687 2.1 24.6 1.0 O B:HOH632 2.1 23.1 1.0 O B:HOH664 2.2 24.6 1.0 CG B:ASP201 3.2 23.3 1.0 OD2 B:ASP201 3.5 22.4 1.0 ZN B:ZN510 3.8 31.3 1.0 OE2 B:GLU230 4.0 25.8 1.0 O B:HOH681 4.1 25.3 1.0 CD2 B:HIS200 4.1 22.9 1.0 O B:HIS200 4.2 23.2 1.0 NE2 B:HIS233 4.2 20.1 1.0 O B:HOH672 4.2 26.4 1.0 OG1 B:THR271 4.2 26.9 1.0 CD2 B:HIS233 4.3 20.1 1.0 C23 B:D5Z508 4.5 31.2 1.0 O B:THR271 4.5 28.7 1.0 OD2 B:ASP318 4.5 32.3 1.0 CB B:ASP201 4.5 24.6 1.0 O B:HOH643 4.5 31.5 1.0 NE2 B:HIS200 4.6 26.8 1.0 CD2 B:HIS204 4.6 22.9 1.0 CG B:GLU230 4.7 23.2 1.0 C22 B:D5Z508 4.8 30.6 1.0 CB B:THR271 4.8 29.2 1.0 CD B:GLU230 4.8 24.7 1.0 NE2 B:HIS204 4.8 24.4 1.0 CD2 B:HIS160 4.8 26.4 1.0 NE2 B:HIS160 4.9 25.5 1.0 CA B:ASP201 4.9 23.8 1.0 C B:HIS200 5.0 22.4 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.