Zinc in PDB 6qgp: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-0769

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-0769, PDB code: 6qgp was solved by A.K.Singh, A.R.Blaazer, L.Zara, I.J.P.De Esch, R.Leurs, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.11 / 1.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.621, 115.344, 68.585, 90.00, 108.32, 90.00
R / Rfree (%)	17.9 / 22.5

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-0769 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-0769 (pdb code 6qgp). 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-0769, PDB code: 6qgp:
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-0769


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-0769 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:23.9 occ:1.00 O A:HOH1196 2.0 24.1 1.0 OD2 A:ASP710 2.1 20.4 1.0 OD1 A:ASP822 2.1 18.2 1.0 O A:HOH1104 2.1 18.9 1.0 NE2 A:HIS673 2.2 21.5 1.0 NE2 A:HIS709 2.2 20.7 1.0 CG A:ASP822 2.9 20.1 1.0 OD2 A:ASP822 3.1 23.8 1.0 CD2 A:HIS673 3.1 22.1 1.0 CD2 A:HIS709 3.1 21.4 1.0 CG A:ASP710 3.2 19.6 1.0 CE1 A:HIS673 3.2 21.0 1.0 CE1 A:HIS709 3.2 21.2 1.0 OD1 A:ASP710 3.7 19.9 1.0 MG A:MG1002 3.7 11.8 1.0 O A:HOH1233 4.1 29.6 1.0 CD2 A:HIS669 4.2 23.3 1.0 O A:HOH1269 4.2 35.5 1.0 CG A:HIS673 4.3 21.2 1.0 CB A:ASP822 4.3 21.3 1.0 ND1 A:HIS673 4.3 22.6 1.0 CG A:HIS709 4.3 21.4 1.0 ND1 A:HIS709 4.3 19.7 1.0 CB A:ASP710 4.4 20.7 1.0 NE2 A:HIS669 4.5 21.3 1.0 CA A:ASP822 4.8 22.5 1.0 CG2 A:VAL677 4.9 21.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-0769


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-0769 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:26.1 occ:1.00 NE2 B:HIS673 2.1 22.7 1.0 OD2 B:ASP710 2.1 23.3 1.0 NE2 B:HIS709 2.2 18.3 1.0 O B:HOH1227 2.2 21.7 1.0 OD1 B:ASP822 2.2 23.8 1.0 O B:HOH1147 2.3 20.0 1.0 CD2 B:HIS709 3.0 16.7 1.0 CD2 B:HIS673 3.1 23.4 1.0 CG B:ASP822 3.1 25.2 1.0 CG B:ASP710 3.1 19.6 1.0 CE1 B:HIS673 3.1 23.7 1.0 OD2 B:ASP822 3.3 27.0 1.0 CE1 B:HIS709 3.3 16.5 1.0 OD1 B:ASP710 3.5 16.4 1.0 MG B:MG1002 3.7 10.9 1.0 O B:HOH1214 3.8 25.8 1.0 O B:HOH1271 4.0 60.9 0.5 CG B:HIS709 4.2 17.7 1.0 CG B:HIS673 4.2 22.4 1.0 ND1 B:HIS673 4.2 22.3 1.0 CD2 B:HIS669 4.2 24.1 1.0 ND1 B:HIS709 4.3 15.0 1.0 CB B:ASP710 4.4 18.9 1.0 CB B:ASP822 4.5 25.2 1.0 NE2 B:HIS669 4.6 26.2 1.0 O B:HOH1168 4.8 19.7 1.0 CG2 B:VAL677 5.0 20.0 1.0 CA B:ASP822 5.0 23.7 1.0

A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-0769 To Be Published.