Magnesium in PDB 6rfw: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039, PDB code: 6rfw 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)	65.11 / 2.18
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.716, 116.553, 68.525, 90.00, 108.17, 90.00
R / Rfree (%)	17.5 / 23.4

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039 (pdb code 6rfw). 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-1039, PDB code: 6rfw:
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-1039


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-1039 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:30.4 occ:1.00 O A:HOH1113 1.9 39.3 1.0 O A:HOH1120 1.9 33.0 1.0 O A:HOH1193 2.0 40.9 1.0 OD1 A:ASP710 2.0 38.1 1.0 O A:HOH1201 2.1 61.5 1.0 O A:HOH1181 2.2 47.5 1.0 CG A:ASP710 3.1 42.4 1.0 O A:HOH1128 3.6 37.6 1.0 OD2 A:ASP710 3.6 40.7 1.0 ZN A:ZN1001 4.0 47.3 1.0 O A:HOH1105 4.1 67.5 1.0 O A:HIS709 4.1 40.0 1.0 OG1 A:THR783 4.1 42.3 1.0 NE2 A:HIS745 4.2 40.5 1.0 O A:HOH1204 4.3 48.6 1.0 OE2 A:GLU742 4.3 48.9 1.0 OD2 A:ASP822 4.3 52.9 1.0 CD2 A:HIS713 4.4 43.4 1.0 CD2 A:HIS709 4.4 45.3 1.0 CB A:ASP710 4.4 39.1 1.0 CD2 A:HIS745 4.5 40.9 1.0 C15 A:K1Q1007 4.6 65.6 1.0 NE2 A:HIS713 4.6 42.5 1.0 CB A:THR783 4.7 43.2 1.0 NE2 A:HIS709 4.7 40.8 1.0 CA A:ASP710 4.8 42.7 1.0 NE2 A:HIS669 4.8 48.1 1.0 CD2 A:HIS669 4.9 44.9 1.0 O A:THR783 4.9 46.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1039


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-1039 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:20.7 occ:1.00 O B:HOH1200 1.9 42.9 1.0 O B:HOH1122 1.9 31.1 1.0 O B:HOH1102 1.9 35.3 1.0 OD1 B:ASP710 1.9 41.0 1.0 O B:HOH1130 2.0 37.6 1.0 O B:HOH1154 2.1 29.2 1.0 CG B:ASP710 2.8 40.6 1.0 OD2 B:ASP710 3.0 39.6 1.0 ZN B:ZN1002 3.7 42.5 1.0 O B:HOH1119 3.8 26.4 1.0 NE2 B:HIS745 4.0 34.7 1.0 O B:HIS709 4.0 35.3 1.0 OE2 B:GLU742 4.1 44.9 1.0 CD2 B:HIS709 4.2 29.6 1.0 CB B:ASP710 4.2 39.8 1.0 OG1 B:THR783 4.2 44.5 1.0 O B:HOH1165 4.3 44.0 1.0 CD2 B:HIS713 4.4 38.7 1.0 CD2 B:HIS745 4.4 33.2 1.0 OD2 B:ASP822 4.5 43.7 1.0 NE2 B:HIS713 4.6 42.2 1.0 NE2 B:HIS709 4.6 28.2 1.0 CD2 B:HIS669 4.6 39.9 1.0 CA B:ASP710 4.7 43.7 1.0 NE2 B:HIS669 4.8 44.5 1.0 C15 B:K1Q1007 4.8 70.0 1.0 CB B:THR783 4.9 38.2 1.0 C B:HIS709 4.9 38.5 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