Magnesium in PDB 6qgp: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-0769

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-0769, PDB code: 6qgp 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)	65.11 / 1.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.621, 115.344, 68.585, 90.00, 108.32, 90.00
R / Rfree (%)	17.9 / 22.5

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-0769 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-0769 (pdb code 6qgp). 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-0769, PDB code: 6qgp:
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-0769


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-0769 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:11.8 occ:1.00 O A:HOH1104 2.0 18.9 1.0 OD1 A:ASP710 2.1 19.9 1.0 O A:HOH1167 2.3 24.7 1.0 O A:HOH1195 2.3 20.6 1.0 O A:HOH1233 2.5 29.6 1.0 O A:HOH1110 2.5 19.3 1.0 CG A:ASP710 3.1 19.6 1.0 OD2 A:ASP710 3.3 20.4 1.0 ZN A:ZN1001 3.7 23.9 1.0 O A:HOH1196 3.9 24.1 1.0 OG1 A:THR783 4.0 19.4 1.0 O A:HIS709 4.1 20.9 1.0 OD2 A:ASP822 4.2 23.8 1.0 OE2 A:GLU742 4.2 28.1 1.0 O A:HOH1289 4.2 37.9 1.0 CD2 A:HIS709 4.2 21.4 1.0 CB A:ASP710 4.4 20.7 1.0 O A:HOH1101 4.4 36.1 1.0 O A:HOH1215 4.5 25.9 1.0 CB A:THR783 4.6 19.6 1.0 CD2 A:HIS713 4.6 22.7 1.0 NE2 A:HIS709 4.6 20.7 1.0 NE2 A:HIS745 4.6 18.6 1.0 CD2 A:HIS745 4.7 17.9 1.0 CA A:ASP710 4.8 20.4 1.0 CD2 A:HIS669 4.9 23.3 1.0 NE2 A:HIS713 4.9 23.0 1.0 NE2 A:HIS669 5.0 21.3 1.0 C A:HIS709 5.0 20.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-0769


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-0769 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:10.9 occ:1.00 O B:HOH1214 1.9 25.8 1.0 O B:HOH1147 1.9 20.0 1.0 O B:HOH1200 2.0 17.3 1.0 O B:HOH1168 2.0 19.7 1.0 OD1 B:ASP710 2.0 16.4 1.0 O B:HOH1160 2.4 18.8 1.0 CG B:ASP710 3.1 19.6 1.0 OD2 B:ASP710 3.5 23.3 1.0 ZN B:ZN1001 3.7 26.1 1.0 O B:HOH1227 3.8 21.7 1.0 O B:HIS709 4.0 20.9 1.0 NE2 B:HIS745 4.0 21.1 1.0 OG1 B:THR783 4.1 21.1 1.0 OE2 B:GLU742 4.1 25.6 1.0 O B:HOH1267 4.2 38.8 1.0 CD2 B:HIS709 4.2 16.7 1.0 OD2 B:ASP822 4.4 27.0 1.0 CD2 B:HIS745 4.4 20.1 1.0 CB B:ASP710 4.4 18.9 1.0 O B:HOH1194 4.5 22.5 1.0 CD2 B:HIS713 4.5 19.6 1.0 CB B:THR783 4.7 19.8 1.0 NE2 B:HIS709 4.7 18.3 1.0 CA B:ASP710 4.8 19.6 1.0 CD2 B:HIS669 4.8 24.1 1.0 NE2 B:HIS713 4.8 21.2 1.0 NE2 B:HIS669 4.9 26.2 1.0 C B:HIS709 4.9 18.9 1.0 CD B:GLU742 5.0 24.5 1.0

A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-0769 To Be Published.