Magnesium in PDB 5g2b: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-008

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-008, PDB code: 5g2b was solved by A.K.Singh, E.S.Anthonyrajah, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.80 / 1.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.360, 115.740, 68.410, 90.00, 108.70, 90.00
R / Rfree (%)	18.3 / 22.1

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-008 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-008 (pdb code 5g2b). 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-008, PDB code: 5g2b:
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-008


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-008 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:14.5 occ:1.00 OD1 A:ASP710 1.9 24.8 1.0 O A:HOH2070 2.0 28.0 1.0 O A:HOH2046 2.0 35.6 1.0 O A:HOH2071 2.0 34.3 1.0 O A:HOH2091 2.1 23.6 1.0 O A:HOH2072 2.2 28.1 1.0 CG A:ASP710 3.1 24.4 1.0 OD2 A:ASP710 3.6 26.4 1.0 ZN A:ZN1001 3.8 33.5 1.0 O A:HOH2045 4.0 31.5 1.0 OE2 A:GLU742 4.1 32.7 1.0 NE2 A:HIS745 4.1 26.9 1.0 OG1 A:THR783 4.1 29.3 1.0 O A:HIS709 4.1 26.8 1.0 CD2 A:HIS709 4.2 28.2 1.0 O A:HOH2074 4.4 34.8 1.0 CB A:ASP710 4.4 29.1 1.0 OD2 A:ASP822 4.4 33.3 1.0 CD2 A:HIS745 4.5 27.3 1.0 O A:HOH2081 4.5 54.1 1.0 CD2 A:HIS713 4.6 28.9 1.0 NE2 A:HIS709 4.6 29.8 1.0 CB A:THR783 4.7 23.8 1.0 C27 A:LQY1003 4.7 36.2 1.0 CA A:ASP710 4.7 31.3 1.0 CD2 A:HIS669 4.8 36.2 1.0 NE2 A:HIS669 4.8 35.9 1.0 C26 A:LQY1003 4.8 43.0 1.0 NE2 A:HIS713 4.9 32.7 1.0 CD A:GLU742 5.0 30.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-008


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-008 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:11.9 occ:1.00 O B:HOH2079 1.8 24.6 1.0 OD1 B:ASP710 1.9 22.3 1.0 O B:HOH2078 2.0 26.4 1.0 O B:HOH2080 2.0 26.0 1.0 O B:HOH2060 2.0 29.7 1.0 O B:HOH2097 2.1 22.3 1.0 CG B:ASP710 3.0 29.2 1.0 OD2 B:ASP710 3.4 32.0 1.0 ZN B:ZN1001 3.8 30.5 1.0 OE2 B:GLU742 4.0 29.7 1.0 O B:HOH2059 4.0 29.9 1.0 O B:HIS709 4.0 25.9 1.0 NE2 B:HIS745 4.1 26.4 1.0 OG1 B:THR783 4.1 29.1 1.0 CD2 B:HIS709 4.2 24.1 1.0 O B:HOH2082 4.3 27.8 1.0 OD2 B:ASP822 4.4 27.7 1.0 CB B:ASP710 4.4 28.1 1.0 O B:HOH2098 4.5 52.1 1.0 CD2 B:HIS745 4.5 25.2 1.0 CD2 B:HIS713 4.5 26.2 1.0 CB B:THR783 4.7 26.4 1.0 NE2 B:HIS709 4.7 23.3 1.0 C26 B:LQY1003 4.7 39.9 1.0 C27 B:LQY1003 4.7 40.2 1.0 CA B:ASP710 4.8 27.6 1.0 NE2 B:HIS669 4.8 30.9 1.0 NE2 B:HIS713 4.8 29.6 1.0 CD2 B:HIS669 4.8 31.3 1.0 O B:HOH2117 4.9 37.9 1.0 CD B:GLU742 4.9 30.6 1.0 C B:HIS709 5.0 25.6 1.0

A.R.Blaazer, A.K.Singh, E.De Heuvel, E.Edink, K.M.Orrling, J.J.N.Veerman, T.Van Den Bergh, C.Jansen, E.Balasubramaniam, W.J.Mooij, H.Custers, M.Sijm, D.N.A.Tagoe, T.D.Kalejaiye, J.C.Munday, H.Tenor, A.Matheeussen, M.Wijtmans, M.Siderius, C.De Graaf, L.Maes, H.P.De Koning, D.S.Bailey, G.J.Sterk, I.J.P.De Esch, D.G.Brown, R.Leurs. Targeting A Subpocket in Trypanosoma Brucei Phosphodiesterase B1 (TBRPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. J. Med. Chem. V. 61 3870 2018.
ISSN: ISSN 1520-4804
PubMed: 29672041
DOI: 10.1021/ACS.JMEDCHEM.7B01670