Magnesium in PDB 6fv9: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-007

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-007, PDB code: 6fv9 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)	79.47 / 2.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.203, 114.619, 68.387, 90.00, 108.36, 90.00
R / Rfree (%)	20.6 / 25.4

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-007 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-007 (pdb code 6fv9). 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-007, PDB code: 6fv9:
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-007


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-007 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:4.4 occ:1.00 O A:HOH1175 1.9 8.7 1.0 O A:HOH1117 1.9 7.5 1.0 O A:HOH1206 1.9 23.0 1.0 O A:HOH1144 2.0 6.8 1.0 OD1 A:ASP710 2.1 10.4 1.0 O A:HOH1136 2.3 7.6 1.0 CG A:ASP710 3.2 11.1 1.0 OD2 A:ASP710 3.6 11.0 1.0 ZN A:ZN1002 3.9 16.7 1.0 OG1 A:THR783 4.0 12.9 1.0 O A:HOH1159 4.1 10.6 1.0 OE2 A:GLU742 4.2 14.0 1.0 NE2 A:HIS745 4.3 14.3 1.0 O A:HIS709 4.3 11.8 1.0 OD2 A:ASP822 4.3 12.2 1.0 CD2 A:HIS709 4.4 11.6 1.0 CD2 A:HIS713 4.5 17.9 1.0 CB A:ASP710 4.6 11.6 1.0 CD2 A:HIS745 4.6 14.4 1.0 C24 A:E8H1006 4.6 30.1 1.0 NE2 A:HIS713 4.6 18.1 1.0 NE2 A:HIS669 4.7 13.5 1.0 CB A:THR783 4.8 13.5 1.0 O A:THR783 4.8 14.6 1.0 CD2 A:HIS669 4.8 13.7 1.0 NE2 A:HIS709 4.8 11.7 1.0 C23 A:E8H1006 4.9 29.7 1.0 CA A:ASP710 5.0 12.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-007


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-007 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:5.2 occ:1.00 O B:HOH1166 1.9 10.1 1.0 O B:HOH1137 2.0 7.2 1.0 OD1 B:ASP710 2.0 12.6 1.0 O B:HOH1164 2.0 7.5 1.0 O B:HOH1196 2.0 8.3 1.0 O B:HOH1194 2.3 17.6 1.0 CG B:ASP710 3.1 13.0 1.0 OD2 B:ASP710 3.4 12.9 1.0 NE2 B:HIS745 3.8 13.4 1.0 ZN B:ZN1002 3.9 24.4 1.0 O B:HIS709 3.9 12.8 1.0 OE2 B:GLU742 4.1 16.6 1.0 CD2 B:HIS745 4.1 13.7 1.0 O B:HOH1121 4.1 8.7 1.0 OG1 B:THR783 4.2 15.0 1.0 CB B:ASP710 4.4 13.2 1.0 O B:HOH1165 4.4 11.5 1.0 CD2 B:HIS709 4.4 12.0 1.0 CD2 B:HIS713 4.4 14.7 1.0 NE2 B:HIS669 4.7 18.0 1.0 NE2 B:HIS713 4.7 14.6 1.0 CA B:ASP710 4.7 13.6 1.0 OD2 B:ASP822 4.8 17.9 1.0 CD2 B:HIS669 4.8 17.8 1.0 CB B:THR783 4.9 15.7 1.0 C B:HIS709 4.9 12.9 1.0 CD B:GLU742 4.9 15.7 1.0 CG B:GLU742 4.9 15.4 1.0 NE2 B:HIS709 4.9 11.7 1.0 CE1 B:HIS745 4.9 13.5 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-007 To Be Published.