Zinc in PDB 6frd: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-637

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-637, PDB code: 6frd 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)	56.74 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.980, 113.480, 68.220, 90.00, 107.89, 90.00
R / Rfree (%)	16.9 / 20.9

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-637 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-637 (pdb code 6frd). 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-637, PDB code: 6frd:
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-637


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-637 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:33.1 occ:1.00 O A:HOH1116 2.0 31.1 1.0 OD1 A:ASP822 2.2 28.5 1.0 OD2 A:ASP710 2.2 25.8 1.0 NE2 A:HIS709 2.2 28.1 1.0 NE2 A:HIS673 2.2 22.4 1.0 O A:HOH1146 2.6 36.3 1.0 CD2 A:HIS709 3.1 24.8 1.0 CG A:ASP822 3.1 26.1 1.0 CG A:ASP710 3.1 25.4 1.0 CE1 A:HIS673 3.2 21.6 1.0 CD2 A:HIS673 3.2 21.6 1.0 OD2 A:ASP822 3.2 25.2 1.0 CE1 A:HIS709 3.3 31.7 1.0 OD1 A:ASP710 3.5 23.5 1.0 MG A:MG1002 3.9 22.9 1.0 O A:HOH1172 4.1 36.4 1.0 CD2 A:HIS669 4.1 26.0 1.0 CG A:HIS709 4.2 25.7 1.0 ND1 A:HIS673 4.3 21.6 1.0 ND1 A:HIS709 4.3 29.1 1.0 CG A:HIS673 4.3 23.0 1.0 CB A:ASP710 4.4 25.1 1.0 CB A:ASP822 4.5 25.5 1.0 NE2 A:HIS669 4.5 24.6 1.0 O A:HOH1123 4.7 19.1 1.0 CA A:ASP822 4.9 25.9 1.0 CG2 A:VAL677 5.0 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-637


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-637 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:31.2 occ:1.00 OD1 B:ASP822 2.1 28.9 1.0 OD2 B:ASP710 2.2 25.7 1.0 NE2 B:HIS673 2.3 22.9 1.0 NE2 B:HIS709 2.3 21.5 1.0 O B:HOH1114 2.3 16.9 1.0 O B:HOH1156 2.8 27.5 1.0 CG B:ASP822 2.9 29.5 1.0 CD2 B:HIS709 3.1 21.0 1.0 CG B:ASP710 3.1 23.0 1.0 OD2 B:ASP822 3.2 30.0 1.0 CE1 B:HIS673 3.2 23.6 1.0 CD2 B:HIS673 3.3 26.9 1.0 CE1 B:HIS709 3.4 21.8 1.0 OD1 B:ASP710 3.5 20.1 1.0 O B:HOH1165 3.8 27.3 1.0 MG B:MG1002 3.8 19.5 1.0 CD2 B:HIS669 4.1 24.9 1.0 CG B:HIS709 4.3 22.3 1.0 CB B:ASP822 4.3 28.2 1.0 ND1 B:HIS673 4.4 22.9 1.0 CB B:ASP710 4.4 22.4 1.0 CG B:HIS673 4.4 23.3 1.0 ND1 B:HIS709 4.4 19.3 1.0 NE2 B:HIS669 4.5 24.9 1.0 O B:HOH1137 4.7 19.3 1.0 O B:HOH1193 4.7 48.0 1.0 CA B:ASP822 4.8 25.9 1.0

A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-637 To Be Published.