Magnesium in PDB 6fdx: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1086

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1086, PDB code: 6fdx 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)	57.10 / 2.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.102, 116.385, 68.310, 90.00, 108.67, 90.00
R / Rfree (%)	16.9 / 23.2

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1086 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-1086 (pdb code 6fdx). 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-1086, PDB code: 6fdx:
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-1086


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-1086 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:37.8 occ:1.00 O A:HOH1101 1.7 35.5 1.0 O A:HOH1110 1.8 66.3 1.0 OD1 A:ASP710 1.9 49.4 1.0 O A:HOH1146 2.1 36.3 1.0 O A:HOH1148 2.2 50.1 1.0 O A:HOH1109 2.2 55.6 1.0 CG A:ASP710 3.0 50.6 1.0 OD2 A:ASP710 3.4 51.9 1.0 O A:HIS709 3.7 40.8 1.0 OG1 A:THR783 3.8 45.5 1.0 ZN A:ZN1001 3.9 56.4 1.0 NE2 A:HIS745 3.9 50.6 1.0 CD2 A:HIS709 4.0 47.6 1.0 OE2 A:GLU742 4.2 63.5 1.0 CB A:ASP710 4.2 50.0 1.0 CD2 A:HIS745 4.3 47.2 1.0 NE2 A:HIS709 4.3 44.2 1.0 CD2 A:HIS713 4.5 45.0 1.0 OD2 A:ASP822 4.5 54.3 1.0 CA A:ASP710 4.5 50.2 1.0 CB A:THR783 4.6 42.9 1.0 C A:HIS709 4.7 49.5 1.0 O A:HOH1154 4.8 50.2 1.0 O A:THR783 4.8 46.2 1.0 O A:HOH1162 4.9 61.2 1.0 CD A:GLU742 4.9 58.1 1.0 CG A:GLU742 4.9 55.9 1.0 CE1 A:HIS745 5.0 48.8 1.0 NE2 A:HIS713 5.0 43.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1086


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-1086 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:25.0 occ:1.00 O B:HOH1106 1.9 37.8 1.0 O B:HOH1156 2.0 41.8 1.0 OD1 B:ASP710 2.0 41.0 1.0 O B:HOH1110 2.0 32.8 1.0 O B:HOH1123 2.1 38.7 1.0 O B:HOH1132 2.2 31.9 1.0 CG B:ASP710 3.0 39.6 1.0 OD2 B:ASP710 3.3 41.8 1.0 ZN B:ZN1001 3.8 45.8 1.0 OE2 B:GLU742 4.0 45.0 1.0 NE2 B:HIS745 4.0 39.9 1.0 O B:HOH1146 4.0 32.0 1.0 OG1 B:THR783 4.1 43.9 1.0 O B:HIS709 4.1 38.4 1.0 O B:HOH1137 4.2 45.0 1.0 CD2 B:HIS709 4.4 36.7 1.0 OD2 B:ASP822 4.4 45.0 1.0 CD2 B:HIS745 4.4 38.2 1.0 CB B:ASP710 4.4 38.9 1.0 CD2 B:HIS713 4.4 42.1 1.0 NE2 B:HIS713 4.7 45.3 1.0 C23 B:D5Z1004 4.7 51.1 1.0 CA B:ASP710 4.7 45.9 1.0 CB B:THR783 4.8 44.1 1.0 NE2 B:HIS709 4.8 35.8 1.0 CD2 B:HIS669 4.8 47.6 1.0 NE2 B:HIS669 4.8 50.1 1.0 CD B:GLU742 4.9 48.0 1.0 C22 B:D5Z1004 4.9 48.5 1.0 O B:THR783 5.0 46.5 1.0 C B:HIS709 5.0 41.7 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-1086 To Be Published.