Magnesium in PDB 6fe3: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439, PDB code: 6fe3 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)	57.41 / 1.62
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.530, 114.820, 68.310, 90.00, 108.25, 90.00
R / Rfree (%)	16.5 / 19

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439 also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439 (pdb code 6fe3). 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-1439, PDB code: 6fe3:
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-1439


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-1439 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:17.1 occ:1.00 O A:HOH1119 2.1 22.8 1.0 O A:HOH1170 2.1 22.1 1.0 OD1 A:ASP710 2.1 20.6 1.0 O A:HOH1281 2.1 25.7 1.0 O A:HOH1197 2.1 23.7 1.0 O A:HOH1223 2.1 22.1 1.0 CG A:ASP710 3.2 19.8 1.0 OD2 A:ASP710 3.6 20.8 1.0 ZN A:ZN1004 3.8 24.6 1.0 NE2 A:HIS745 4.1 21.1 1.0 OG1 A:THR783 4.1 21.4 1.0 O A:HOH1224 4.1 26.5 1.0 O A:HIS709 4.2 19.8 1.0 OE2 A:GLU742 4.2 27.4 1.0 CD2 A:HIS709 4.3 20.6 1.0 OD2 A:ASP822 4.3 26.6 1.0 O A:HOH1274 4.4 25.5 1.0 CD2 A:HIS745 4.5 19.1 1.0 CB A:ASP710 4.5 20.9 1.0 O A:HOH1103 4.6 38.6 1.0 CD2 A:HIS713 4.6 23.8 1.0 NE2 A:HIS709 4.6 19.2 1.0 CB A:THR783 4.6 20.9 1.0 NE2 A:HIS669 4.8 25.4 1.0 C23 A:D681003 4.8 29.5 1.0 CD2 A:HIS669 4.8 26.7 1.0 CA A:ASP710 4.8 22.0 1.0 NE2 A:HIS713 4.9 22.2 1.0 C24 A:D681003 5.0 30.9 1.0 O A:THR783 5.0 22.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439


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-1439 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1005 b:18.6 occ:1.00 OD1 B:ASP710 2.0 23.5 1.0 O B:HOH1121 2.0 25.2 1.0 O B:HOH1267 2.1 26.6 1.0 O B:HOH1202 2.1 21.9 1.0 O B:HOH1160 2.1 24.2 1.0 O B:HOH1109 2.1 24.5 1.0 CG B:ASP710 2.9 21.9 1.0 OD2 B:ASP710 3.1 22.1 1.0 ZN B:ZN1004 3.7 25.8 1.0 O B:HOH1206 3.9 29.0 1.0 NE2 B:HIS745 4.1 21.0 1.0 OE2 B:GLU742 4.1 28.6 1.0 OG1 B:THR783 4.1 24.1 1.0 O B:HIS709 4.2 22.4 1.0 CD2 B:HIS709 4.2 20.6 1.0 O B:HOH1295 4.2 43.2 1.0 CB B:ASP710 4.3 22.1 1.0 O B:HOH1232 4.3 26.7 1.0 OD2 B:ASP822 4.3 26.9 1.0 CD2 B:HIS745 4.5 20.1 1.0 CD2 B:HIS713 4.5 22.2 1.0 NE2 B:HIS709 4.6 19.7 1.0 CD2 B:HIS669 4.7 25.1 1.0 CB B:THR783 4.7 23.6 1.0 NE2 B:HIS669 4.8 24.6 1.0 CA B:ASP710 4.8 21.0 1.0 NE2 B:HIS713 4.8 22.4 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-1439 To Be Published.