Zinc in PDB 6rb6: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053, PDB code: 6rb6 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)	69.57 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	147.516, 115.070, 63.780, 90.00, 109.39, 90.00
R / Rfree (%)	16.5 / 19.7

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053 (pdb code 6rb6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053, PDB code: 6rb6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:23.0 occ:1.00 NE2 A:HIS709 2.0 18.8 1.0 O A:HOH1145 2.0 21.2 1.0 OD2 A:ASP710 2.1 20.3 1.0 OD1 A:ASP822 2.2 17.1 1.0 NE2 A:HIS673 2.2 17.6 1.0 O A:HOH1241 2.3 27.7 1.0 CD2 A:HIS709 2.8 19.4 1.0 CE1 A:HIS709 3.1 19.2 1.0 CG A:ASP822 3.1 19.3 1.0 CD2 A:HIS673 3.2 19.0 1.0 CE1 A:HIS673 3.2 19.7 1.0 CG A:ASP710 3.2 17.2 1.0 OD2 A:ASP822 3.4 24.6 1.0 OD1 A:ASP710 3.8 17.6 1.0 MG A:MG1001 3.8 8.4 1.0 CG A:HIS709 3.9 18.2 1.0 O A:HOH1287 4.0 36.3 1.0 O A:HOH1277 4.0 27.9 1.0 ND1 A:HIS709 4.0 17.5 1.0 ND1 A:HIS673 4.3 19.8 1.0 CD2 A:HIS669 4.3 22.6 1.0 CG A:HIS673 4.3 18.6 1.0 CB A:ASP710 4.4 18.9 1.0 CB A:ASP822 4.5 19.0 1.0 NE2 A:HIS669 4.8 23.6 1.0 O A:HOH1123 4.8 21.1 1.0 CA A:ASP822 4.9 19.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-053 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:23.4 occ:1.00 OD1 B:ASP822 2.1 18.5 1.0 OD2 B:ASP710 2.2 18.5 1.0 NE2 B:HIS673 2.2 17.6 1.0 O B:HOH1118 2.2 19.8 1.0 NE2 B:HIS709 2.3 16.5 1.0 O B:HOH1213 2.3 26.0 1.0 CG B:ASP822 3.0 20.9 1.0 CD2 B:HIS709 3.1 15.5 1.0 CG B:ASP710 3.1 17.9 1.0 CD2 B:HIS673 3.2 17.8 1.0 CE1 B:HIS673 3.2 17.8 1.0 OD2 B:ASP822 3.3 24.1 1.0 CE1 B:HIS709 3.3 17.3 1.0 OD1 B:ASP710 3.5 17.5 1.0 MG B:MG1003 3.7 7.2 1.0 O B:HOH1245 3.9 24.6 1.0 O B:HOH1250 4.1 31.1 1.0 CG B:HIS709 4.3 16.4 1.0 CD2 B:HIS669 4.3 19.9 1.0 ND1 B:HIS673 4.3 18.2 1.0 CG B:HIS673 4.3 17.5 1.0 ND1 B:HIS709 4.4 17.8 1.0 CB B:ASP822 4.4 19.5 1.0 CB B:ASP710 4.4 18.6 1.0 NE2 B:HIS669 4.7 20.4 1.0 O B:HOH1139 4.7 20.4 1.0 CA B:ASP822 4.9 19.2 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