Zinc 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
Magnesium	(Mg)	2 atoms

The binding sites of Zinc 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 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-1039, PDB code: 6rfw:
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-1039


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-1039 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:47.3 occ:1.00 O A:HOH1128 1.8 37.6 1.0 NE2 A:HIS709 2.1 40.8 1.0 OD1 A:ASP822 2.1 49.8 1.0 OD2 A:ASP710 2.1 40.7 1.0 NE2 A:HIS673 2.3 52.6 1.0 O A:HOH1113 2.3 39.3 1.0 CG A:ASP822 3.0 49.4 1.0 CD2 A:HIS709 3.0 45.3 1.0 CE1 A:HIS709 3.0 47.0 1.0 CD2 A:HIS673 3.1 46.6 1.0 CG A:ASP710 3.1 42.4 1.0 OD2 A:ASP822 3.3 52.9 1.0 CE1 A:HIS673 3.4 52.7 1.0 OD1 A:ASP710 3.5 38.1 1.0 MG A:MG1002 4.0 30.4 1.0 O A:HOH1208 4.0 53.2 1.0 ND1 A:HIS709 4.1 40.3 1.0 CG A:HIS709 4.2 46.1 1.0 CD2 A:HIS669 4.2 44.9 1.0 CG A:HIS673 4.3 50.6 1.0 CB A:ASP822 4.3 55.4 1.0 O A:HOH1201 4.3 61.5 1.0 CB A:ASP710 4.3 39.1 1.0 ND1 A:HIS673 4.4 53.9 1.0 NE2 A:HIS669 4.6 48.1 1.0 O A:HOH1120 4.6 33.0 1.0 CG2 A:VAL677 4.8 42.7 1.0 CA A:ASP822 4.8 48.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1002 b:42.5 occ:1.00 OD2 B:ASP710 2.0 39.6 1.0 NE2 B:HIS709 2.0 28.2 1.0 O B:HOH1119 2.1 26.4 1.0 NE2 B:HIS673 2.2 35.3 1.0 OD1 B:ASP822 2.2 40.5 1.0 O B:HOH1122 2.5 31.1 1.0 CD2 B:HIS709 2.9 29.6 1.0 CG B:ASP710 3.1 40.6 1.0 CG B:ASP822 3.1 41.4 1.0 CD2 B:HIS673 3.1 42.4 1.0 CE1 B:HIS673 3.2 46.2 1.0 CE1 B:HIS709 3.2 33.4 1.0 OD2 B:ASP822 3.4 43.7 1.0 MG B:MG1003 3.7 20.7 1.0 OD1 B:ASP710 3.8 41.0 1.0 O B:HOH1200 3.9 42.9 1.0 CG B:HIS709 4.1 31.5 1.0 CD2 B:HIS669 4.1 39.9 1.0 CB B:ASP710 4.2 39.8 1.0 ND1 B:HIS709 4.2 25.2 1.0 CG B:HIS673 4.3 42.0 1.0 ND1 B:HIS673 4.3 38.1 1.0 O B:HOH1194 4.4 51.9 1.0 CB B:ASP822 4.4 43.9 1.0 NE2 B:HIS669 4.5 44.5 1.0 O B:HOH1102 4.6 35.3 1.0 CA B:ASP822 4.9 40.6 1.0 CG2 B:VAL677 4.9 38.4 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