Zinc in PDB 5l8c: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-039

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-039, PDB code: 5l8c was solved by A.K.Singh, E.S.Anthonyrajah, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.06 / 2.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.600, 115.130, 68.630, 90.00, 108.12, 90.00
R / Rfree (%)	19.5 / 23.7

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-039 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-039 (pdb code 5l8c). 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-039, PDB code: 5l8c:
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-039


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-039 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:39.4 occ:1.00 OD2 A:ASP710 2.0 32.5 1.0 OD1 A:ASP822 2.1 37.2 1.0 NE2 A:HIS673 2.3 35.5 1.0 O A:HOH1126 2.3 38.8 1.0 NE2 A:HIS709 2.3 46.3 1.0 O A:HOH1166 2.3 43.5 1.0 CG A:ASP822 3.0 35.3 1.0 CG A:ASP710 3.0 35.5 1.0 OD2 A:ASP822 3.1 39.2 1.0 CD2 A:HIS709 3.1 42.2 1.0 CE1 A:HIS673 3.2 34.8 1.0 CD2 A:HIS673 3.3 34.7 1.0 CE1 A:HIS709 3.4 41.6 1.0 OD1 A:ASP710 3.5 27.2 1.0 MG A:MG1002 3.8 20.2 1.0 O A:HOH1199 4.0 39.1 1.0 O A:HOH1227 4.1 52.9 1.0 CD2 A:HIS669 4.2 39.5 1.0 CG A:HIS709 4.3 43.7 1.0 ND1 A:HIS673 4.3 35.7 1.0 CB A:ASP710 4.3 32.4 1.0 CB A:ASP822 4.4 40.2 1.0 CG A:HIS673 4.4 34.2 1.0 ND1 A:HIS709 4.4 39.6 1.0 NE2 A:HIS669 4.6 38.8 1.0 O A:HOH1115 4.7 32.0 1.0 CA A:ASP822 4.9 38.3 1.0 CG2 A:VAL677 5.0 36.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-039


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-039 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:34.7 occ:1.00 OD2 B:ASP710 2.0 37.8 1.0 OD1 B:ASP822 2.2 30.5 1.0 NE2 B:HIS709 2.3 24.8 1.0 NE2 B:HIS673 2.3 29.4 1.0 O B:HOH1186 2.4 25.9 1.0 O B:HOH1133 2.5 31.1 1.0 CG B:ASP822 3.0 35.7 1.0 CG B:ASP710 3.1 32.7 1.0 CD2 B:HIS709 3.1 26.6 1.0 OD2 B:ASP822 3.2 37.0 1.0 CE1 B:HIS673 3.2 33.5 1.0 CD2 B:HIS673 3.3 30.7 1.0 CE1 B:HIS709 3.4 28.2 1.0 OD1 B:ASP710 3.5 27.0 1.0 MG B:MG1002 3.7 16.7 1.0 O B:HOH1216 3.9 38.9 1.0 CD2 B:HIS669 4.1 35.1 1.0 O B:HOH1241 4.2 63.1 1.0 CG B:HIS709 4.3 27.8 1.0 CB B:ASP710 4.3 32.7 1.0 ND1 B:HIS673 4.4 31.8 1.0 ND1 B:HIS709 4.4 24.7 1.0 CB B:ASP822 4.4 36.4 1.0 CG B:HIS673 4.4 31.3 1.0 NE2 B:HIS669 4.5 38.0 1.0 O B:HOH1128 4.6 29.5 1.0 CA B:ASP822 4.9 35.5 1.0

A.R.Blaazer, A.K.Singh, E.De Heuvel, E.Edink, K.M.Orrling, J.J.N.Veerman, T.Van Den Bergh, C.Jansen, E.Balasubramaniam, W.J.Mooij, H.Custers, M.Sijm, D.N.A.Tagoe, T.D.Kalejaiye, J.C.Munday, H.Tenor, A.Matheeussen, M.Wijtmans, M.Siderius, C.De Graaf, L.Maes, H.P.De Koning, D.S.Bailey, G.J.Sterk, I.J.P.De Esch, D.G.Brown, R.Leurs. Targeting A Subpocket in Trypanosoma Brucei Phosphodiesterase B1 (TBRPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. J. Med. Chem. V. 61 3870 2018.
ISSN: ISSN 1520-4804
PubMed: 29672041
DOI: 10.1021/ACS.JMEDCHEM.7B01670