Magnesium in PDB 6ftm: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-048

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-048, PDB code: 6ftm 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)	70.28 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.052, 114.730, 63.800, 90.00, 109.43, 90.00
R / Rfree (%)	15.7 / 19.8

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-048 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-048 (pdb code 6ftm). 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-048, PDB code: 6ftm:
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-048


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-048 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:5.4 occ:1.00 O A:HOH1114 2.0 18.1 1.0 O A:HOH1120 2.0 21.6 1.0 O A:HOH1230 2.0 24.1 1.0 OD1 A:ASP710 2.1 17.2 1.0 O A:HOH1169 2.1 18.7 1.0 O A:HOH1167 2.2 18.8 1.0 CG A:ASP710 3.1 17.6 1.0 OD2 A:ASP710 3.6 18.3 1.0 ZN A:ZN1002 3.8 23.6 1.0 O A:HOH1208 3.9 25.8 1.0 OG1 A:THR783 4.1 17.3 1.0 NE2 A:HIS745 4.1 18.2 1.0 OE2 A:GLU742 4.1 24.9 1.0 O A:HOH1211 4.2 20.4 1.0 CD2 A:HIS709 4.3 16.1 1.0 O A:HIS709 4.3 18.2 1.0 CD2 A:HIS713 4.4 15.6 1.0 OD2 A:ASP822 4.4 21.3 1.0 CD2 A:HIS745 4.5 18.6 1.0 CB A:ASP710 4.5 19.1 1.0 NE2 A:HIS713 4.5 17.7 1.0 CB A:THR783 4.7 19.7 1.0 NE2 A:HIS709 4.7 16.4 1.0 O A:THR783 4.8 20.1 1.0 O A:HOH1144 4.8 40.7 1.0 CA A:ASP710 4.9 17.6 1.0 C22 A:E6Z1026 4.9 33.5 1.0 CG A:GLU742 5.0 20.9 1.0 CD A:GLU742 5.0 23.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-048


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-048 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:8.6 occ:1.00 O B:HOH1135 2.0 19.8 1.0 OD1 B:ASP710 2.0 18.0 1.0 O B:HOH1125 2.0 22.1 1.0 O B:HOH1158 2.1 27.4 1.0 O B:HOH1159 2.1 21.6 1.0 O B:HOH1239 2.2 30.6 1.0 CG B:ASP710 3.1 20.6 1.0 OD2 B:ASP710 3.6 20.8 1.0 O B:HOH1203 3.8 26.9 1.0 ZN B:ZN1002 3.8 25.5 1.0 OG1 B:THR783 4.1 21.2 1.0 NE2 B:HIS745 4.1 17.5 1.0 OE2 B:GLU742 4.1 28.2 1.0 O B:HIS709 4.2 16.8 1.0 O B:HOH1194 4.4 24.4 1.0 CD2 B:HIS709 4.4 18.7 1.0 OD2 B:ASP822 4.4 23.2 1.0 CD2 B:HIS745 4.4 19.9 1.0 CB B:ASP710 4.5 20.4 1.0 CD2 B:HIS713 4.6 21.3 1.0 CB B:THR783 4.6 22.2 1.0 NE2 B:HIS709 4.9 19.2 1.0 NE2 B:HIS713 4.9 22.2 1.0 CA B:ASP710 4.9 19.8 1.0 CD2 B:HIS669 4.9 22.8 1.0 C22 B:E6Z1013 4.9 38.1 1.0

E.De Heuvel, A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-048 To Be Published.