Zinc in PDB 6fe3: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439, PDB code: 6fe3 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)	57.41 / 1.62
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.530, 114.820, 68.310, 90.00, 108.25, 90.00
R / Rfree (%)	16.5 / 19

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439 also contains other interesting chemical elements:

Fluorine	(F)	4 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-1439 (pdb code 6fe3). 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-1439, PDB code: 6fe3:
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-1439


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-1439 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:24.6 occ:1.00 O A:HOH1119 2.1 22.8 1.0 OD1 A:ASP822 2.1 19.9 1.0 NE2 A:HIS673 2.1 20.4 1.0 OD2 A:ASP710 2.2 20.8 1.0 NE2 A:HIS709 2.2 19.2 1.0 O A:HOH1224 2.2 26.5 1.0 CG A:ASP822 3.0 24.3 1.0 CE1 A:HIS673 3.1 23.1 1.0 CD2 A:HIS709 3.1 20.6 1.0 CD2 A:HIS673 3.1 22.8 1.0 CE1 A:HIS709 3.2 20.1 1.0 CG A:ASP710 3.2 19.8 1.0 OD2 A:ASP822 3.3 26.6 1.0 OD1 A:ASP710 3.6 20.6 1.0 MG A:MG1005 3.8 17.1 1.0 O A:HOH1281 4.0 25.7 1.0 CD2 A:HIS669 4.2 26.7 1.0 O A:HOH1176 4.2 37.6 1.0 ND1 A:HIS673 4.2 21.5 1.0 CG A:HIS709 4.3 19.9 1.0 CG A:HIS673 4.3 22.4 1.0 ND1 A:HIS709 4.3 18.8 1.0 NE2 A:HIS669 4.4 25.4 1.0 CB A:ASP822 4.4 24.4 1.0 CB A:ASP710 4.5 20.9 1.0 O A:HOH1170 4.8 22.1 1.0 CG2 A:VAL677 4.9 20.9 1.0 CA A:ASP822 4.9 21.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439


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-1439 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:25.8 occ:1.00 OD2 B:ASP710 2.0 22.1 1.0 O B:HOH1121 2.1 25.2 1.0 NE2 B:HIS673 2.1 21.0 1.0 OD1 B:ASP822 2.2 20.2 1.0 NE2 B:HIS709 2.2 19.7 1.0 O B:HOH1206 2.2 29.0 1.0 CG B:ASP822 3.0 23.2 1.0 CD2 B:HIS709 3.0 20.6 1.0 CE1 B:HIS673 3.1 22.2 1.0 CD2 B:HIS673 3.1 22.1 1.0 CG B:ASP710 3.2 21.9 1.0 CE1 B:HIS709 3.2 21.7 1.0 OD2 B:ASP822 3.3 26.9 1.0 MG B:MG1005 3.7 18.6 1.0 OD1 B:ASP710 3.8 23.5 1.0 O B:HOH1267 4.0 26.6 1.0 CD2 B:HIS669 4.2 25.1 1.0 CG B:HIS709 4.2 20.4 1.0 ND1 B:HIS673 4.2 21.3 1.0 ND1 B:HIS709 4.3 20.9 1.0 CG B:HIS673 4.3 21.1 1.0 CB B:ASP710 4.3 22.1 1.0 CB B:ASP822 4.4 21.0 1.0 NE2 B:HIS669 4.4 24.6 1.0 O B:HOH1109 4.8 24.5 1.0 CA B:ASP822 4.9 21.3 1.0 CG2 B:VAL677 5.0 23.5 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-1439 To Be Published.