Magnesium in PDB 6fds: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-226

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-226, PDB code: 6fds 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)	79.98 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.720, 120.170, 68.170, 90.00, 108.05, 90.00
R / Rfree (%)	19.3 / 24

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-226 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-226 (pdb code 6fds). 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-226, PDB code: 6fds:
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-226


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-226 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1006 b:27.2 occ:1.00 O A:HOH1176 1.8 35.2 1.0 OD1 A:ASP710 1.9 35.7 1.0 O A:HOH1141 1.9 43.9 1.0 O A:HOH1169 2.0 36.8 1.0 O A:HOH1118 2.0 35.2 1.0 O A:HOH1133 2.1 36.8 1.0 CG A:ASP710 3.0 46.1 1.0 OD2 A:ASP710 3.5 48.8 1.0 ZN A:ZN1005 3.8 43.8 1.0 O A:HOH1150 3.9 38.7 1.0 NE2 A:HIS745 4.1 49.8 1.0 O A:HIS709 4.1 39.6 1.0 O A:HOH1138 4.1 51.1 1.0 OG1 A:THR783 4.2 47.5 1.0 CD2 A:HIS709 4.2 31.2 1.0 OE2 A:GLU742 4.3 52.9 1.0 CB A:ASP710 4.4 45.5 1.0 OD2 A:ASP822 4.5 39.1 1.0 CD2 A:HIS713 4.5 46.4 1.0 CD2 A:HIS745 4.5 41.0 1.0 C24 A:D5T1002 4.6 57.6 1.0 NE2 A:HIS709 4.7 31.9 1.0 CA A:ASP710 4.7 45.1 1.0 CB A:THR783 4.7 42.5 1.0 NE2 A:HIS713 4.8 45.4 1.0 NE2 A:HIS669 4.8 49.5 1.0 CD2 A:HIS669 4.9 52.9 1.0 C23 A:D5T1002 4.9 59.3 1.0 C A:HIS709 5.0 41.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-226


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-226 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:17.5 occ:1.00 O B:HOH1123 1.7 27.3 1.0 O B:HOH1119 1.7 28.2 1.0 O B:HOH1154 1.9 32.5 1.0 OD1 B:ASP710 2.0 30.9 1.0 O B:HOH1138 2.0 30.6 1.0 O B:HOH1158 2.1 33.1 1.0 CG B:ASP710 3.2 39.9 1.0 OD2 B:ASP710 3.6 36.8 1.0 ZN B:ZN1002 3.8 42.6 1.0 O B:HOH1151 4.0 31.8 1.0 NE2 B:HIS745 4.0 32.2 1.0 OE2 B:GLU742 4.1 43.9 1.0 O B:HIS709 4.1 33.0 1.0 OG1 B:THR783 4.1 35.4 1.0 CD2 B:HIS709 4.3 30.0 1.0 CD2 B:HIS745 4.4 32.6 1.0 OD2 B:ASP822 4.4 43.2 1.0 O B:HOH1160 4.5 41.0 1.0 CD2 B:HIS713 4.5 32.6 1.0 CB B:ASP710 4.5 35.6 1.0 C24 B:D5T1006 4.6 93.1 1.0 NE2 B:HIS709 4.7 30.6 1.0 CB B:THR783 4.8 36.6 1.0 CA B:ASP710 4.8 34.0 1.0 NE2 B:HIS713 4.8 36.2 1.0 C23 B:D5T1006 4.9 84.5 1.0 NE2 B:HIS669 4.9 43.9 1.0 O B:HOH1134 4.9 47.3 1.0 CD2 B:HIS669 4.9 39.8 1.0 CD B:GLU742 4.9 47.6 1.0 CG B:GLU742 5.0 44.0 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. TBRPDEB1 Structure with Inhibitor Npd-226 To Be Published.