Magnesium in PDB 6qgu: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1361

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1361, PDB code: 6qgu was solved by A.K.Singh, A.R.Blaazer, L.Zara, I.J.P.De Esch, R.Leurs, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.40 / 1.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.467, 114.814, 68.314, 90.00, 108.23, 90.00
R / Rfree (%)	15.9 / 19.5

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1361 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-1361 (pdb code 6qgu). 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-1361, PDB code: 6qgu:
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-1361


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-1361 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:15.6 occ:1.00 O A:HOH1143 2.0 24.9 1.0 OD1 A:ASP710 2.0 20.4 1.0 O A:HOH1122 2.2 24.5 1.0 O A:HOH1283 2.2 28.4 1.0 O A:HOH1199 2.3 23.0 1.0 O A:HOH1125 2.4 23.4 1.0 CG A:ASP710 3.1 20.6 1.0 OD2 A:ASP710 3.5 22.6 1.0 ZN A:ZN1001 3.7 25.7 1.0 O A:HOH1210 3.9 28.2 1.0 NE2 A:HIS745 4.0 22.3 1.0 OE2 A:GLU742 4.1 30.6 1.0 O A:HIS709 4.1 19.9 1.0 OG1 A:THR783 4.2 22.9 1.0 CD2 A:HIS709 4.2 20.2 1.0 OD2 A:ASP822 4.3 29.9 1.0 O A:HOH1322 4.4 42.5 1.0 O A:HOH1248 4.4 30.7 1.0 CB A:ASP710 4.4 21.7 1.0 CD2 A:HIS745 4.5 21.0 1.0 CD2 A:HIS713 4.5 25.3 1.0 O A:HOH1102 4.5 40.2 1.0 NE2 A:HIS709 4.6 19.5 1.0 CB A:THR783 4.7 20.3 1.0 CA A:ASP710 4.7 21.8 1.0 NE2 A:HIS669 4.8 25.4 1.0 CD2 A:HIS669 4.8 26.4 1.0 NE2 A:HIS713 4.9 22.7 1.0 C A:HIS709 5.0 19.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1361


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-1361 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:15.9 occ:1.00 O B:HOH1130 2.0 26.1 1.0 OD1 B:ASP710 2.0 20.8 1.0 O B:HOH1165 2.1 23.6 1.0 O B:HOH1179 2.2 21.8 1.0 O B:HOH1237 2.4 28.9 1.0 O B:HOH1200 2.4 22.8 1.0 CG B:ASP710 3.1 22.5 1.0 OD2 B:ASP710 3.5 22.2 1.0 ZN B:ZN1001 3.7 26.8 1.0 O B:HOH1228 3.9 28.8 1.0 NE2 B:HIS745 4.1 20.9 1.0 O B:HOH1290 4.1 41.3 1.0 O B:HIS709 4.1 22.1 1.0 OE2 B:GLU742 4.1 31.3 1.0 OG1 B:THR783 4.1 24.7 1.0 CD2 B:HIS709 4.2 20.4 1.0 OD2 B:ASP822 4.3 31.7 1.0 O B:HOH1216 4.4 27.7 1.0 CD2 B:HIS745 4.4 21.9 1.0 CB B:ASP710 4.4 21.6 1.0 CD2 B:HIS713 4.5 23.9 1.0 NE2 B:HIS709 4.5 21.9 1.0 CB B:THR783 4.7 24.5 1.0 CA B:ASP710 4.7 21.1 1.0 CD2 B:HIS669 4.7 26.4 1.0 NE2 B:HIS713 4.8 23.0 1.0 NE2 B:HIS669 4.9 25.2 1.0 C B:HIS709 5.0 23.4 1.0 CD B:GLU742 5.0 28.8 1.0

A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1361 To Be Published.