Magnesium in PDB 6rgk: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-055

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-055, PDB code: 6rgk 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)	79.57 / 2.03
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.780, 116.480, 68.610, 90.00, 108.32, 90.00
R / Rfree (%)	18 / 23.3

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-055 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-055 (pdb code 6rgk). 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-055, PDB code: 6rgk:
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-055


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-055 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:25.6 occ:1.00 O A:HOH1147 1.9 38.0 1.0 O A:HOH1141 2.0 30.9 1.0 O A:HOH1222 2.0 51.2 1.0 O A:HOH1180 2.0 39.1 1.0 OD1 A:ASP710 2.0 35.4 1.0 O A:HOH1216 2.2 38.2 1.0 CG A:ASP710 3.1 36.7 1.0 OD2 A:ASP710 3.6 34.9 1.0 O A:HOH1138 3.6 39.2 1.0 ZN A:ZN1001 3.9 41.1 1.0 O A:HIS709 4.0 36.0 1.0 NE2 A:HIS745 4.1 38.7 1.0 OG1 A:THR783 4.2 38.9 1.0 O A:HOH1212 4.3 40.8 1.0 CD2 A:HIS709 4.3 39.8 1.0 OD2 A:ASP822 4.4 47.2 1.0 CD2 A:HIS713 4.4 38.1 1.0 CB A:ASP710 4.4 36.7 1.0 OE2 A:GLU742 4.5 52.9 1.0 CD2 A:HIS745 4.6 36.0 1.0 NE2 A:HIS709 4.6 37.1 1.0 NE2 A:HIS713 4.7 37.1 1.0 CD2 A:HIS669 4.7 41.7 1.0 CA A:ASP710 4.7 40.9 1.0 NE2 A:HIS669 4.8 42.7 1.0 CB A:THR783 4.8 32.8 1.0 C A:HIS709 5.0 38.9 1.0 C26 A:K3N1008 5.0 60.5 1.0 O A:THR783 5.0 41.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-055


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-055 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:20.2 occ:1.00 O B:HOH1127 1.9 32.5 1.0 OD1 B:ASP710 1.9 36.0 1.0 O B:HOH1207 2.0 42.5 1.0 O B:HOH1173 2.0 31.9 1.0 O B:HOH1104 2.0 36.1 1.0 O B:HOH1148 2.1 35.0 1.0 CG B:ASP710 3.0 37.2 1.0 OD2 B:ASP710 3.4 39.3 1.0 ZN B:ZN1001 3.9 36.9 1.0 O B:HOH1193 3.9 23.7 1.0 NE2 B:HIS745 4.0 32.1 1.0 OE2 B:GLU742 4.0 40.6 1.0 OG1 B:THR783 4.2 37.4 1.0 O B:HIS709 4.2 31.1 1.0 O B:HOH1159 4.3 36.3 1.0 CD2 B:HIS709 4.3 26.5 1.0 CB B:ASP710 4.3 35.9 1.0 CD2 B:HIS745 4.4 31.3 1.0 OD2 B:ASP822 4.4 38.5 1.0 CD2 B:HIS713 4.5 34.0 1.0 NE2 B:HIS709 4.7 26.7 1.0 CB B:THR783 4.7 34.6 1.0 CA B:ASP710 4.7 36.0 1.0 NE2 B:HIS713 4.8 37.9 1.0 CD2 B:HIS669 4.8 38.8 1.0 CD B:GLU742 4.9 39.2 1.0 NE2 B:HIS669 4.9 40.7 1.0 C26 B:K3N1007 4.9 46.3 1.0 O B:HOH1146 5.0 52.9 1.0 CG B:GLU742 5.0 36.4 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