Zinc in PDB 6gxq: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335, PDB code: 6gxq 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)	57.28 / 1.96
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.876, 114.424, 68.232, 90.00, 108.36, 90.00
R / Rfree (%)	20 / 24.4

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335 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-1335 (pdb code 6gxq). 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-1335, PDB code: 6gxq:
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-1335


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-1335 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:36.0 occ:1.00 NE2 A:HIS673 2.1 26.6 1.0 O A:HOH1127 2.1 32.6 1.0 OD1 A:ASP822 2.2 29.9 1.0 OD2 A:ASP710 2.2 29.9 1.0 NE2 A:HIS709 2.2 25.8 1.0 O A:HOH1175 2.4 37.3 1.0 CG A:ASP822 3.1 31.4 1.0 CD2 A:HIS673 3.1 27.4 1.0 CD2 A:HIS709 3.1 23.7 1.0 CE1 A:HIS673 3.1 27.6 1.0 CG A:ASP710 3.1 27.2 1.0 CE1 A:HIS709 3.3 24.8 1.0 OD2 A:ASP822 3.3 36.3 1.0 OD1 A:ASP710 3.5 29.1 1.0 MG A:MG1001 3.8 27.3 1.0 O A:HOH1259 3.9 35.2 1.0 O A:HOH1258 4.1 50.4 1.0 ND1 A:HIS673 4.2 30.1 1.0 CD2 A:HIS669 4.2 27.9 1.0 CG A:HIS673 4.2 29.2 1.0 CG A:HIS709 4.3 23.3 1.0 ND1 A:HIS709 4.3 24.4 1.0 CB A:ASP710 4.4 29.5 1.0 CB A:ASP822 4.4 29.8 1.0 NE2 A:HIS669 4.5 29.0 1.0 O A:HOH1134 4.8 27.4 1.0 CG2 A:VAL677 4.9 23.0 1.0 CA A:ASP822 4.9 28.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335


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-1335 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:36.9 occ:1.00 O B:HOH1199 1.8 30.6 1.0 NE2 B:HIS673 2.1 27.8 1.0 OD1 B:ASP822 2.2 29.1 1.0 OD2 B:ASP710 2.2 32.1 1.0 O B:HOH1185 2.2 33.3 1.0 NE2 B:HIS709 2.2 26.5 1.0 CD2 B:HIS673 3.1 28.1 1.0 CD2 B:HIS709 3.1 25.0 1.0 CE1 B:HIS673 3.1 27.6 1.0 CG B:ASP822 3.1 31.9 1.0 CG B:ASP710 3.1 28.9 1.0 CE1 B:HIS709 3.3 26.9 1.0 O B:HOH1237 3.4 37.6 1.0 OD2 B:ASP822 3.5 35.0 1.0 OD1 B:ASP710 3.5 28.3 1.0 MG B:MG1002 3.8 29.9 1.0 O B:HOH1242 3.9 27.4 1.0 ND1 B:HIS673 4.2 30.0 1.0 CG B:HIS673 4.2 27.3 1.0 CD2 B:HIS669 4.2 30.6 1.0 CG B:HIS709 4.3 22.7 1.0 ND1 B:HIS709 4.3 23.1 1.0 CB B:ASP710 4.4 27.9 1.0 CB B:ASP822 4.5 30.6 1.0 NE2 B:HIS669 4.6 31.7 1.0 CG2 B:VAL677 4.8 30.6 1.0 CA B:ASP822 4.9 29.6 1.0 O B:HOH1112 4.9 27.3 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