Zinc in PDB 6rgk: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-055

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-055, PDB code: 6rgk 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)	79.57 / 2.03
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.780, 116.480, 68.610, 90.00, 108.32, 90.00
R / Rfree (%)	18 / 23.3

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-055 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-055 (pdb code 6rgk). 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-055, PDB code: 6rgk:
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-055


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-055 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:41.1 occ:1.00 O A:HOH1138 1.9 39.2 1.0 NE2 A:HIS709 2.0 37.1 1.0 OD1 A:ASP822 2.1 41.0 1.0 OD2 A:ASP710 2.1 34.9 1.0 NE2 A:HIS673 2.2 39.2 1.0 O A:HOH1147 2.3 38.0 1.0 CD2 A:HIS709 3.0 39.8 1.0 CE1 A:HIS709 3.0 39.1 1.0 CG A:ASP822 3.1 44.9 1.0 CD2 A:HIS673 3.1 41.3 1.0 CG A:ASP710 3.1 36.7 1.0 CE1 A:HIS673 3.2 40.8 1.0 OD2 A:ASP822 3.4 47.2 1.0 OD1 A:ASP710 3.6 35.4 1.0 MG A:MG1002 3.9 25.6 1.0 O A:HOH1249 4.0 49.1 1.0 ND1 A:HIS709 4.1 35.8 1.0 CG A:HIS709 4.1 37.5 1.0 O A:HOH1222 4.1 51.2 1.0 CG A:HIS673 4.3 41.3 1.0 CD2 A:HIS669 4.3 41.7 1.0 ND1 A:HIS673 4.3 44.2 1.0 CB A:ASP710 4.4 36.7 1.0 CB A:ASP822 4.4 45.0 1.0 NE2 A:HIS669 4.7 42.7 1.0 O A:HOH1141 4.7 30.9 1.0 CG2 A:VAL677 4.7 38.3 1.0 CA A:ASP822 4.9 38.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-055


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-055 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:36.9 occ:1.00 O B:HOH1193 2.0 23.7 1.0 OD2 B:ASP710 2.1 39.3 1.0 NE2 B:HIS673 2.1 29.4 1.0 NE2 B:HIS709 2.2 26.7 1.0 OD1 B:ASP822 2.2 34.5 1.0 O B:HOH1104 2.4 36.1 1.0 CD2 B:HIS673 3.0 32.6 1.0 CD2 B:HIS709 3.1 26.5 1.0 CG B:ASP822 3.1 36.7 1.0 CG B:ASP710 3.1 37.2 1.0 CE1 B:HIS673 3.2 34.1 1.0 CE1 B:HIS709 3.2 31.3 1.0 OD2 B:ASP822 3.3 38.5 1.0 OD1 B:ASP710 3.5 36.0 1.0 O B:HOH1208 3.8 40.2 1.0 MG B:MG1002 3.9 20.2 1.0 O B:HOH1207 4.1 42.5 1.0 CD2 B:HIS669 4.2 38.8 1.0 CG B:HIS673 4.2 33.0 1.0 CG B:HIS709 4.2 27.8 1.0 ND1 B:HIS673 4.2 32.9 1.0 ND1 B:HIS709 4.3 25.6 1.0 CB B:ASP710 4.3 35.9 1.0 CB B:ASP822 4.5 38.3 1.0 NE2 B:HIS669 4.5 40.7 1.0 O B:HOH1127 4.6 32.5 1.0 CA B:ASP822 4.9 35.0 1.0 CG2 B:VAL677 4.9 32.0 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