Magnesium in PDB 6rb6: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053, PDB code: 6rb6 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)	69.57 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.516, 115.070, 63.780, 90.00, 109.39, 90.00
R / Rfree (%)	16.5 / 19.7

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053 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-053 (pdb code 6rb6). 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-053, PDB code: 6rb6:
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-053


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-053 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:8.4 occ:1.00 O A:HOH1196 2.0 23.0 1.0 O A:HOH1123 2.0 21.1 1.0 O A:HOH1190 2.0 19.7 1.0 O A:HOH1145 2.1 21.2 1.0 O A:HOH1277 2.1 27.9 1.0 OD1 A:ASP710 2.2 17.6 1.0 CG A:ASP710 3.1 17.2 1.0 OD2 A:ASP710 3.3 20.3 1.0 ZN A:ZN1002 3.8 23.0 1.0 CD2 A:HIS709 4.1 19.4 1.0 O A:HOH1241 4.1 27.7 1.0 OG1 A:THR783 4.1 20.6 1.0 NE2 A:HIS745 4.1 17.9 1.0 OE2 A:GLU742 4.1 32.6 1.0 O A:HIS709 4.2 19.1 1.0 O A:HOH1240 4.4 24.6 1.0 CD2 A:HIS745 4.4 17.8 1.0 OD2 A:ASP822 4.4 24.6 1.0 CB A:ASP710 4.5 18.9 1.0 NE2 A:HIS709 4.5 18.8 1.0 CD2 A:HIS713 4.6 20.7 1.0 CB A:THR783 4.7 22.7 1.0 C27 A:JX21014 4.8 38.1 1.0 O A:HOH1225 4.8 46.4 1.0 CA A:ASP710 4.9 19.4 1.0 CD2 A:HIS669 5.0 22.6 1.0 NE2 A:HIS713 5.0 20.0 1.0 CG A:GLU742 5.0 25.4 1.0 CD A:GLU742 5.0 29.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053


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-053 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:7.2 occ:1.00 O B:HOH1118 1.9 19.8 1.0 O B:HOH1139 2.0 20.4 1.0 O B:HOH1245 2.0 24.6 1.0 O B:HOH1226 2.1 18.6 1.0 OD1 B:ASP710 2.1 17.5 1.0 O B:HOH1203 2.1 22.2 1.0 CG B:ASP710 3.2 17.9 1.0 OD2 B:ASP710 3.6 18.5 1.0 ZN B:ZN1004 3.7 23.4 1.0 O B:HOH1213 3.9 26.0 1.0 OE2 B:GLU742 4.1 26.6 1.0 OG1 B:THR783 4.1 21.4 1.0 O B:HOH1225 4.1 24.4 1.0 CD2 B:HIS709 4.2 15.5 1.0 O B:HIS709 4.3 16.9 1.0 OD2 B:ASP822 4.3 24.1 1.0 NE2 B:HIS745 4.4 16.7 1.0 CD2 B:HIS713 4.5 18.2 1.0 CB B:ASP710 4.5 18.6 1.0 CD2 B:HIS745 4.6 16.8 1.0 NE2 B:HIS709 4.7 16.5 1.0 CB B:THR783 4.7 19.4 1.0 NE2 B:HIS713 4.7 17.1 1.0 C27 B:JX21012 4.9 44.4 1.0 CA B:ASP710 4.9 17.3 1.0 O B:THR783 4.9 19.1 1.0 O B:HOH1177 4.9 39.9 1.0 CD2 B:HIS669 5.0 19.9 1.0

E.De Heuvel, A.K.Singh, P.Boronat, A.J.Kooistra, T.Van Der Meer, P.Sadek, A.R.Blaazer, N.C.Shaner, D.S.Bindels, G.Caljon, L.Maes, G.J.Sterk, M.Siderius, M.Oberholzer, I.J.P.De Esch, D.G.Brown, R.Leurs. Alkynamide Phthalazinones As A New Class of TBRPDEB1 Inhibitors (Part 2). Bioorg.Med.Chem. V. 27 4013 2019.
ISSN: ESSN 1464-3391
PubMed: 31378593
DOI: 10.1016/J.BMC.2019.06.026