Magnesium in PDB 6rfn: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1018

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1018, PDB code: 6rfn 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)	65.21 / 2.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.713, 116.081, 68.669, 90.00, 108.26, 90.00
R / Rfree (%)	16.4 / 22.2

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1018 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-1018 (pdb code 6rfn). 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-1018, PDB code: 6rfn:
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-1018


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-1018 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:22.0 occ:1.00 O A:HOH1117 1.9 38.5 1.0 O A:HOH1144 1.9 32.7 1.0 O A:HOH1224 2.0 45.4 1.0 OD1 A:ASP710 2.0 34.3 1.0 O A:HOH1213 2.1 29.8 1.0 O A:HOH1200 2.2 35.8 1.0 CG A:ASP710 3.2 38.2 1.0 OD2 A:ASP710 3.7 39.6 1.0 ZN A:ZN1001 3.9 41.7 1.0 O A:HOH1193 4.0 46.1 1.0 NE2 A:HIS745 4.0 36.5 1.0 O A:HIS709 4.0 39.0 1.0 OG1 A:THR783 4.2 35.8 1.0 O A:HOH1226 4.2 36.2 1.0 OD2 A:ASP822 4.3 41.8 1.0 OE2 A:GLU742 4.3 46.1 1.0 CD2 A:HIS709 4.3 38.7 1.0 CB A:ASP710 4.4 33.4 1.0 CD2 A:HIS745 4.5 35.5 1.0 CD2 A:HIS713 4.5 36.5 1.0 NE2 A:HIS709 4.7 37.0 1.0 CA A:ASP710 4.7 40.8 1.0 NE2 A:HIS713 4.7 36.7 1.0 CB A:THR783 4.8 35.0 1.0 C24 A:K3W1009 4.8 70.8 1.0 CD2 A:HIS669 4.8 43.0 1.0 NE2 A:HIS669 4.9 45.7 1.0 C A:HIS709 4.9 36.4 1.0 O A:THR783 5.0 47.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1018


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-1018 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:16.7 occ:1.00 O B:HOH1128 1.8 22.3 1.0 O B:HOH1125 1.9 31.7 1.0 OD1 B:ASP710 2.0 32.2 1.0 O B:HOH1231 2.0 43.5 1.0 O B:HOH1139 2.1 31.8 1.0 O B:HOH1150 2.1 29.5 1.0 CG B:ASP710 2.9 34.0 1.0 OD2 B:ASP710 3.2 37.1 1.0 O B:HOH1172 3.7 25.8 1.0 ZN B:ZN1001 3.8 38.5 1.0 NE2 B:HIS745 3.9 31.5 1.0 O B:HIS709 4.0 31.8 1.0 OG1 B:THR783 4.1 33.8 1.0 OE2 B:GLU742 4.1 43.1 1.0 O B:HOH1143 4.2 38.8 1.0 CD2 B:HIS709 4.3 26.4 1.0 CB B:ASP710 4.3 32.8 1.0 OD2 B:ASP822 4.4 43.1 1.0 CD2 B:HIS745 4.4 29.4 1.0 CD2 B:HIS713 4.5 35.6 1.0 NE2 B:HIS709 4.7 27.7 1.0 C24 B:K3W1006 4.7 69.9 1.0 CA B:ASP710 4.7 34.7 1.0 CD2 B:HIS669 4.8 37.6 1.0 CB B:THR783 4.8 34.9 1.0 NE2 B:HIS713 4.8 35.1 1.0 O B:HOH1170 4.9 54.8 1.0 NE2 B:HIS669 5.0 44.1 1.0 C B:HIS709 5.0 34.2 1.0 O B:THR783 5.0 39.8 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