Zinc in PDB 6rfn: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1018

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1018, PDB code: 6rfn 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)	65.21 / 2.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.713, 116.081, 68.669, 90.00, 108.26, 90.00
R / Rfree (%)	16.4 / 22.2

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1018 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-1018 (pdb code 6rfn). 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-1018, PDB code: 6rfn:
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-1018


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-1018 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:41.7 occ:1.00 OD1 A:ASP822 2.1 41.2 1.0 OD2 A:ASP710 2.1 39.6 1.0 NE2 A:HIS709 2.1 37.0 1.0 O A:HOH1193 2.2 46.1 1.0 NE2 A:HIS673 2.2 39.9 1.0 O A:HOH1117 2.2 38.5 1.0 CG A:ASP822 2.9 43.3 1.0 CD2 A:HIS709 3.1 38.7 1.0 OD2 A:ASP822 3.1 41.8 1.0 CG A:ASP710 3.1 38.2 1.0 CD2 A:HIS673 3.1 38.7 1.0 CE1 A:HIS709 3.2 41.5 1.0 CE1 A:HIS673 3.2 37.8 1.0 OD1 A:ASP710 3.5 34.3 1.0 MG A:MG1002 3.9 22.0 1.0 O A:HOH1251 4.1 48.8 1.0 O A:HOH1224 4.1 45.4 1.0 CG A:HIS709 4.2 38.1 1.0 ND1 A:HIS709 4.2 38.2 1.0 CD2 A:HIS669 4.3 43.0 1.0 ND1 A:HIS673 4.3 41.3 1.0 CG A:HIS673 4.3 40.7 1.0 CB A:ASP822 4.3 46.6 1.0 CB A:ASP710 4.5 33.4 1.0 NE2 A:HIS669 4.6 45.7 1.0 O A:HOH1144 4.6 32.7 1.0 CA A:ASP822 4.8 41.7 1.0 CG2 A:VAL677 4.8 36.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1018


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-1018 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:38.5 occ:1.00 O B:HOH1172 2.0 25.8 1.0 OD2 B:ASP710 2.0 37.1 1.0 OD1 B:ASP822 2.1 37.6 1.0 NE2 B:HIS709 2.2 27.7 1.0 NE2 B:HIS673 2.2 32.7 1.0 O B:HOH1128 2.5 22.3 1.0 CG B:ASP822 3.0 39.5 1.0 CD2 B:HIS709 3.0 26.4 1.0 CG B:ASP710 3.1 34.0 1.0 CE1 B:HIS673 3.2 39.3 1.0 OD2 B:ASP822 3.2 43.1 1.0 CD2 B:HIS673 3.2 38.3 1.0 CE1 B:HIS709 3.3 30.3 1.0 OD1 B:ASP710 3.7 32.2 1.0 MG B:MG1002 3.8 16.7 1.0 O B:HOH1232 3.8 51.9 1.0 O B:HOH1231 4.1 43.5 1.0 CG B:HIS709 4.2 27.6 1.0 CD2 B:HIS669 4.2 37.6 1.0 CB B:ASP710 4.3 32.8 1.0 ND1 B:HIS673 4.3 34.1 1.0 ND1 B:HIS709 4.3 25.4 1.0 CG B:HIS673 4.3 36.1 1.0 CB B:ASP822 4.4 38.5 1.0 NE2 B:HIS669 4.6 44.1 1.0 O B:HOH1125 4.7 31.7 1.0 CA B:ASP822 4.9 38.1 1.0 CG2 B:VAL677 4.9 34.9 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