Magnesium in PDB 6gxq: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335, PDB code: 6gxq 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)	57.28 / 1.96
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.876, 114.424, 68.232, 90.00, 108.36, 90.00
R / Rfree (%)	20 / 24.4

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335 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-1335 (pdb code 6gxq). 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-1335, PDB code: 6gxq:
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-1335


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-1335 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:27.3 occ:1.00 OD1 A:ASP710 2.0 29.1 1.0 O A:HOH1259 2.0 35.2 1.0 O A:HOH1203 2.0 26.6 1.0 O A:HOH1134 2.1 27.4 1.0 O A:HOH1127 2.1 32.6 1.0 O A:HOH1227 2.1 32.1 1.0 CG A:ASP710 3.1 27.2 1.0 OD2 A:ASP710 3.5 29.9 1.0 ZN A:ZN1002 3.8 36.0 1.0 O A:HOH1175 3.9 37.3 1.0 NE2 A:HIS745 4.0 30.4 1.0 O A:HIS709 4.0 27.3 1.0 OG1 A:THR783 4.1 26.5 1.0 OE2 A:GLU742 4.2 30.4 1.0 CD2 A:HIS709 4.3 23.7 1.0 CD2 A:HIS745 4.3 28.0 1.0 CB A:ASP710 4.4 29.5 1.0 O A:HOH1200 4.4 30.9 1.0 OD2 A:ASP822 4.4 36.3 1.0 CD2 A:HIS713 4.5 31.1 1.0 O A:HOH1103 4.5 47.0 1.0 CB A:THR783 4.6 24.2 1.0 CA A:ASP710 4.6 29.1 1.0 NE2 A:HIS709 4.7 25.8 1.0 C25 A:FFZ1005 4.7 39.5 1.0 CD2 A:HIS669 4.8 27.9 1.0 NE2 A:HIS713 4.9 30.0 1.0 C A:HIS709 4.9 26.1 1.0 NE2 A:HIS669 4.9 29.0 1.0 CE1 A:HIS745 5.0 30.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335


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-1335 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:29.9 occ:1.00 OD1 B:ASP710 2.0 28.3 1.0 O B:HOH1185 2.0 33.3 1.0 O B:HOH1242 2.0 27.4 1.0 O B:HOH1170 2.0 26.2 1.0 O B:HOH1112 2.1 27.3 1.0 O B:HOH1154 2.2 28.6 1.0 CG B:ASP710 3.0 28.9 1.0 OD2 B:ASP710 3.5 32.1 1.0 O B:HOH1199 3.6 30.6 1.0 ZN B:ZN1003 3.8 36.9 1.0 NE2 B:HIS745 3.9 23.6 1.0 O B:HIS709 3.9 27.4 1.0 OG1 B:THR783 4.2 32.6 1.0 OE2 B:GLU742 4.2 34.0 1.0 CD2 B:HIS709 4.2 25.0 1.0 O B:HOH1235 4.3 29.2 1.0 CD2 B:HIS745 4.3 24.0 1.0 CB B:ASP710 4.3 27.9 1.0 CD2 B:HIS713 4.5 27.4 1.0 OD2 B:ASP822 4.5 35.0 1.0 CA B:ASP710 4.6 25.9 1.0 NE2 B:HIS709 4.6 26.5 1.0 CB B:THR783 4.7 29.7 1.0 NE2 B:HIS713 4.8 28.5 1.0 CD2 B:HIS669 4.8 30.6 1.0 C B:HIS709 4.9 26.0 1.0 NE2 B:HIS669 5.0 31.7 1.0 CE1 B:HIS745 5.0 24.1 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