Zinc in PDB 6ftm: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-048

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-048, PDB code: 6ftm 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)	70.28 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.052, 114.730, 63.800, 90.00, 109.43, 90.00
R / Rfree (%)	15.7 / 19.8

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-048 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-048 (pdb code 6ftm). 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-048, PDB code: 6ftm:
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-048


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-048 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:23.6 occ:1.00 OD1 A:ASP822 2.2 21.9 1.0 NE2 A:HIS673 2.2 19.2 1.0 O A:HOH1120 2.2 21.6 1.0 NE2 A:HIS709 2.2 16.4 1.0 OD2 A:ASP710 2.2 18.3 1.0 O A:HOH1208 2.3 25.8 1.0 CG A:ASP822 3.0 22.6 1.0 CD2 A:HIS709 3.1 16.1 1.0 CE1 A:HIS673 3.1 17.3 1.0 CG A:ASP710 3.2 17.6 1.0 CD2 A:HIS673 3.2 20.2 1.0 OD2 A:ASP822 3.3 21.3 1.0 CE1 A:HIS709 3.3 18.4 1.0 OD1 A:ASP710 3.5 17.2 1.0 MG A:MG1001 3.8 5.4 1.0 O A:HOH1230 3.9 24.1 1.0 ND1 A:HIS673 4.3 16.0 1.0 CD2 A:HIS669 4.3 21.0 1.0 CG A:HIS709 4.3 17.2 1.0 ND1 A:HIS709 4.3 16.5 1.0 O A:HOH1218 4.3 24.8 1.0 CG A:HIS673 4.4 18.1 1.0 CB A:ASP710 4.4 19.1 1.0 CB A:ASP822 4.5 21.3 1.0 NE2 A:HIS669 4.7 21.7 1.0 O A:HOH1114 4.7 18.1 1.0 CA A:ASP822 5.0 19.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-048


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-048 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:25.5 occ:1.00 O B:HOH1203 2.1 26.9 1.0 O B:HOH1135 2.1 19.8 1.0 OD2 B:ASP710 2.2 20.8 1.0 NE2 B:HIS673 2.2 21.3 1.0 OD1 B:ASP822 2.2 19.6 1.0 NE2 B:HIS709 2.3 19.2 1.0 CD2 B:HIS709 3.1 18.7 1.0 CG B:ASP822 3.1 21.3 1.0 CG B:ASP710 3.1 20.6 1.0 CE1 B:HIS673 3.2 23.0 1.0 CD2 B:HIS673 3.2 22.6 1.0 OD2 B:ASP822 3.3 23.2 1.0 CE1 B:HIS709 3.4 19.1 1.0 OD1 B:ASP710 3.5 18.0 1.0 MG B:MG1001 3.8 8.6 1.0 O B:HOH1239 4.0 30.6 1.0 CG B:HIS709 4.3 18.5 1.0 CD2 B:HIS669 4.3 22.8 1.0 ND1 B:HIS673 4.3 23.7 1.0 CG B:HIS673 4.4 20.9 1.0 CB B:ASP710 4.4 20.4 1.0 O B:HOH1242 4.4 29.7 1.0 ND1 B:HIS709 4.4 16.6 1.0 CB B:ASP822 4.5 22.3 1.0 NE2 B:HIS669 4.8 23.9 1.0 O B:HOH1125 4.8 22.1 1.0 CA B:ASP822 5.0 20.3 1.0

E.De Heuvel, A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-048 To Be Published.