Magnesium in PDB 6fdw: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-356

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-356, PDB code: 6fdw 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)	33.91 / 1.96
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.690, 119.260, 67.970, 90.00, 108.38, 90.00
R / Rfree (%)	19 / 23.7

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-356 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-356 (pdb code 6fdw). 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-356, PDB code: 6fdw:
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-356


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-356 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:32.2 occ:1.00 O A:HOH1107 1.7 29.6 1.0 O A:HOH1140 2.0 41.0 1.0 OD1 A:ASP710 2.0 34.3 1.0 O A:HOH1134 2.1 43.0 1.0 O A:HOH1193 2.2 40.6 1.0 O A:HOH1105 2.2 38.9 1.0 CG A:ASP710 3.0 35.1 1.0 OD2 A:ASP710 3.2 33.5 1.0 ZN A:ZN1002 3.9 41.5 1.0 OG1 A:THR783 3.9 43.2 1.0 OE2 A:GLU742 3.9 41.8 1.0 O A:HOH1165 4.0 41.0 1.0 O A:HIS709 4.2 36.5 1.0 O A:HOH1147 4.2 48.0 1.0 CD2 A:HIS709 4.3 32.2 1.0 O A:HOH1114 4.3 63.6 1.0 CB A:ASP710 4.4 35.3 1.0 OD2 A:ASP822 4.4 42.2 1.0 NE2 A:HIS745 4.4 42.0 1.0 C21 A:D621001 4.6 50.3 1.0 CB A:THR783 4.6 36.0 1.0 CD2 A:HIS745 4.6 41.5 1.0 CD2 A:HIS713 4.6 37.4 1.0 O A:HOH1204 4.6 49.9 1.0 NE2 A:HIS709 4.7 34.0 1.0 O A:THR783 4.8 39.2 1.0 CA A:ASP710 4.9 38.6 1.0 NE2 A:HIS669 4.9 40.5 1.0 C20 A:D621001 4.9 49.1 1.0 CD A:GLU742 4.9 48.6 1.0 NE2 A:HIS713 4.9 39.1 1.0 CD2 A:HIS669 5.0 40.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-356


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-356 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:22.1 occ:1.00 O B:HOH1107 2.0 29.8 1.0 O B:HOH1182 2.0 33.1 1.0 O B:HOH1166 2.0 33.4 1.0 O B:HOH1109 2.0 34.5 1.0 O B:HOH1146 2.0 36.2 1.0 OD1 B:ASP710 2.1 32.2 1.0 CG B:ASP710 3.0 37.7 1.0 OD2 B:ASP710 3.3 33.9 1.0 ZN B:ZN1002 3.8 36.7 1.0 O B:HOH1158 4.0 30.2 1.0 OE2 B:GLU742 4.0 33.9 1.0 OG1 B:THR783 4.1 34.0 1.0 O B:HIS709 4.1 32.6 1.0 NE2 B:HIS745 4.2 32.9 1.0 O B:HOH1178 4.3 31.9 1.0 CD2 B:HIS709 4.3 27.8 1.0 OD2 B:ASP822 4.4 35.0 1.0 CB B:ASP710 4.4 33.1 1.0 CD2 B:HIS745 4.5 32.3 1.0 CD2 B:HIS713 4.6 34.5 1.0 NE2 B:HIS709 4.7 30.1 1.0 CB B:THR783 4.7 34.2 1.0 NE2 B:HIS669 4.7 32.1 1.0 C21 B:D621001 4.8 49.0 1.0 CA B:ASP710 4.8 33.7 1.0 CD2 B:HIS669 4.8 35.6 1.0 O B:THR783 4.9 31.1 1.0 C20 B:D621001 4.9 45.9 1.0 NE2 B:HIS713 4.9 33.3 1.0 CD B:GLU742 4.9 38.2 1.0 CG B:GLU742 5.0 33.0 1.0 C B:HIS709 5.0 35.5 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-356 To Be Published.