Magnesium in PDB 7a28: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617, PDB code: 7a28 was solved by A.K.Singh, A.R.Blaazer, L.Zara, I.J.P.De Esch, R.Leurs, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.33 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.99, 116.53, 69.15, 90, 108.58, 90
R / Rfree (%)	17.4 / 20.2

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617 (pdb code 7a28). 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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617, PDB code: 7a28:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617


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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:12.2 occ:1.00 OD1 A:ASP710 2.0 26.4 1.0 O A:HOH1197 2.0 24.1 1.0 O A:HOH1138 2.3 28.1 1.0 O A:HOH1174 2.3 23.8 1.0 O A:HOH1276 2.4 39.8 1.0 O A:HOH1147 2.4 25.6 1.0 CG A:ASP710 3.2 27.0 1.0 OD2 A:ASP710 3.6 28.3 1.0 ZN A:ZN1002 3.8 30.8 1.0 NE2 A:HIS745 4.1 25.6 1.0 O A:HIS709 4.1 21.9 1.0 OG1 A:THR783 4.2 25.9 1.0 OE2 A:GLU742 4.3 33.0 1.0 O A:HOH1311 4.3 48.0 1.0 CD2 A:HIS709 4.3 25.2 1.0 O A:HOH1262 4.4 47.6 1.0 O A:HOH1249 4.4 29.5 1.0 CB A:ASP710 4.5 26.6 1.0 OD2 A:ASP822 4.5 32.0 1.0 CD2 A:HIS745 4.5 26.8 1.0 CD2 A:HIS713 4.6 29.1 1.0 O A:HOH1127 4.7 47.9 1.0 NE2 A:HIS709 4.7 25.6 1.0 CB A:THR783 4.7 22.3 1.0 CA A:ASP710 4.8 28.1 1.0 NE2 A:HIS669 4.8 25.8 1.0 CD2 A:HIS669 4.9 28.2 1.0 NE2 A:HIS713 4.9 26.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617


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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:11.4 occ:1.00 O B:HOH1171 1.9 28.2 1.0 OD1 B:ASP710 2.1 22.4 1.0 O B:HOH1244 2.2 29.0 1.0 O B:HOH1158 2.3 23.8 1.0 O B:HOH1201 2.4 23.4 1.0 O B:HOH1117 2.5 26.9 1.0 CG B:ASP710 3.2 26.2 1.0 OD2 B:ASP710 3.6 28.7 1.0 ZN B:ZN1002 3.8 31.5 1.0 O B:HOH1260 4.1 44.3 1.0 O B:HOH1197 4.1 29.6 1.0 NE2 B:HIS745 4.1 23.3 1.0 OE2 B:GLU742 4.2 29.4 1.0 OG1 B:THR783 4.2 29.5 1.0 O B:HIS709 4.2 25.0 1.0 O B:HOH1229 4.3 30.3 1.0 CD2 B:HIS709 4.4 22.2 1.0 OD2 B:ASP822 4.4 32.2 1.0 CB B:ASP710 4.5 23.7 1.0 CD2 B:HIS745 4.5 25.4 1.0 CD2 B:HIS713 4.7 26.5 1.0 NE2 B:HIS709 4.7 24.4 1.0 CB B:THR783 4.8 27.5 1.0 CD2 B:HIS669 4.8 30.9 1.0 O B:HOH1257 4.9 46.7 1.0 NE2 B:HIS669 4.9 29.0 1.0 CA B:ASP710 4.9 23.6 1.0

A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617 To Be Published.