Magnesium in PDB 6frd: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-637

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-637, PDB code: 6frd 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)	56.74 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.980, 113.480, 68.220, 90.00, 107.89, 90.00
R / Rfree (%)	16.9 / 20.9

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-637 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-637 (pdb code 6frd). 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-637, PDB code: 6frd:
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-637


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-637 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:22.9 occ:1.00 O A:HOH1123 2.1 19.1 1.0 O A:HOH1127 2.1 36.2 1.0 O A:HOH1116 2.2 31.1 1.0 O A:HOH1172 2.2 36.4 1.0 O A:HOH1150 2.2 27.9 1.0 OD1 A:ASP710 2.2 23.5 1.0 CG A:ASP710 3.3 25.4 1.0 OD2 A:ASP710 3.8 25.8 1.0 OE2 A:GLU742 3.9 45.7 1.0 ZN A:ZN1001 3.9 33.1 1.0 OG1 A:THR783 4.1 21.6 1.0 NE2 A:HIS745 4.1 26.2 1.0 O A:HIS709 4.3 25.1 1.0 O A:HOH1159 4.3 28.1 1.0 O A:HOH1146 4.3 36.3 1.0 CD2 A:HIS713 4.4 26.6 1.0 OD2 A:ASP822 4.4 25.2 1.0 CD2 A:HIS745 4.4 23.6 1.0 CD2 A:HIS709 4.4 24.8 1.0 CB A:ASP710 4.6 25.1 1.0 NE2 A:HIS713 4.6 27.3 1.0 CB A:THR783 4.7 25.0 1.0 CD A:GLU742 4.8 38.0 1.0 CD2 A:HIS669 4.9 26.0 1.0 NE2 A:HIS709 4.9 28.1 1.0 CA A:ASP710 4.9 24.9 1.0 NE2 A:HIS669 4.9 24.6 1.0 CG A:GLU742 5.0 33.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-637


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-637 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:19.5 occ:1.00 O B:HOH1114 1.9 16.9 1.0 O B:HOH1137 2.0 19.3 1.0 O B:HOH1165 2.0 27.3 1.0 OD1 B:ASP710 2.1 20.1 1.0 O B:HOH1150 2.2 22.2 1.0 O B:HOH1159 2.3 20.7 1.0 CG B:ASP710 3.2 23.0 1.0 OD2 B:ASP710 3.6 25.7 1.0 O B:HOH1193 3.7 48.0 1.0 ZN B:ZN1001 3.8 31.2 1.0 OG1 B:THR783 4.1 25.3 1.0 NE2 B:HIS745 4.1 26.6 1.0 OE2 B:GLU742 4.1 30.3 1.0 O B:HIS709 4.1 22.2 1.0 O B:HOH1175 4.3 29.7 1.0 CD2 B:HIS709 4.3 21.0 1.0 OD2 B:ASP822 4.3 30.0 1.0 CD2 B:HIS713 4.4 25.1 1.0 CD2 B:HIS745 4.4 25.3 1.0 CB B:ASP710 4.5 22.4 1.0 CB B:THR783 4.6 25.6 1.0 O B:HOH1156 4.6 27.5 1.0 NE2 B:HIS713 4.6 25.0 1.0 NE2 B:HIS709 4.7 21.5 1.0 CA B:ASP710 4.8 22.9 1.0 O B:THR783 4.9 26.6 1.0 CD B:GLU742 5.0 31.9 1.0 C B:HIS709 5.0 21.8 1.0 CG B:GLU742 5.0 28.1 1.0

A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-637 To Be Published.