Zinc in PDB 6fds: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-226

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-226, PDB code: 6fds 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)	79.98 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.720, 120.170, 68.170, 90.00, 108.05, 90.00
R / Rfree (%)	19.3 / 24

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-226 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-226 (pdb code 6fds). 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-226, PDB code: 6fds:
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-226


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-226 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1005 b:43.8 occ:1.00 O A:HOH1133 2.0 36.8 1.0 NE2 A:HIS673 2.1 42.9 1.0 OD2 A:ASP710 2.2 48.8 1.0 NE2 A:HIS709 2.2 31.9 1.0 OD1 A:ASP822 2.3 43.3 1.0 O A:HOH1150 2.3 38.7 1.0 CE1 A:HIS673 3.0 46.2 1.0 CD2 A:HIS709 3.1 31.2 1.0 CD2 A:HIS673 3.1 41.2 1.0 CG A:ASP710 3.1 46.1 1.0 CG A:ASP822 3.2 39.5 1.0 CE1 A:HIS709 3.3 32.9 1.0 OD2 A:ASP822 3.4 39.1 1.0 OD1 A:ASP710 3.6 35.7 1.0 MG A:MG1006 3.8 27.2 1.0 O A:HOH1169 4.0 36.8 1.0 ND1 A:HIS673 4.2 36.3 1.0 CG A:HIS673 4.2 43.9 1.0 CD2 A:HIS669 4.2 52.9 1.0 CG A:HIS709 4.3 33.5 1.0 ND1 A:HIS709 4.3 29.8 1.0 CB A:ASP710 4.4 45.5 1.0 O A:HOH1155 4.4 53.7 1.0 NE2 A:HIS669 4.5 49.5 1.0 CB A:ASP822 4.6 42.1 1.0 O A:HOH1118 4.7 35.2 1.0 C24 A:D5T1002 4.9 57.6 1.0 O A:HOH1176 4.9 35.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-226


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-226 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:42.6 occ:1.00 O B:HOH1151 2.2 31.8 1.0 OD2 B:ASP710 2.2 36.8 1.0 OD1 B:ASP822 2.2 37.6 1.0 NE2 B:HIS709 2.2 30.6 1.0 NE2 B:HIS673 2.2 39.1 1.0 O B:HOH1123 2.4 27.3 1.0 CD2 B:HIS709 3.0 30.0 1.0 CG B:ASP822 3.0 42.9 1.0 CG B:ASP710 3.1 39.9 1.0 CE1 B:HIS673 3.2 36.7 1.0 CD2 B:HIS673 3.2 40.2 1.0 OD2 B:ASP822 3.2 43.2 1.0 CE1 B:HIS709 3.3 33.4 1.0 OD1 B:ASP710 3.5 30.9 1.0 MG B:MG1001 3.8 17.5 1.0 O B:HOH1154 3.8 32.5 1.0 CG B:HIS709 4.2 28.2 1.0 CD2 B:HIS669 4.3 39.8 1.0 ND1 B:HIS673 4.3 35.8 1.0 CG B:HIS673 4.3 39.2 1.0 ND1 B:HIS709 4.3 26.5 1.0 O B:HOH1120 4.3 37.6 0.5 CB B:ASP822 4.4 44.8 1.0 CB B:ASP710 4.5 35.6 1.0 NE2 B:HIS669 4.5 43.9 1.0 O B:HOH1119 4.5 28.2 1.0 C24 B:D5T1006 4.7 93.1 1.0 O B:HOH1158 4.9 33.1 1.0 CA B:ASP822 4.9 43.2 1.0

I.G.Salado, C.Moreno, G.Sakaine, A.K.Singh, A.R.Blaazer, M.Siderius, A.Matheeussen, S.Gul, L.Maes, R.Leurs, D.G.Brown, K.Augustyns. TBRPDEB1 Structure with Inhibitor Npd-226 To Be Published.