Zinc in PDB 7a28: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617, PDB code: 7a28 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)	80.33 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.99, 116.53, 69.15, 90, 108.58, 90
R / Rfree (%)	17.4 / 20.2

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617 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-617 (pdb code 7a28). 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-617, PDB code: 7a28:
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-617


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-617 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:30.8 occ:1.00 O A:HOH1197 2.1 24.1 1.0 OD1 A:ASP822 2.1 24.7 1.0 NE2 A:HIS673 2.2 22.6 1.0 OD2 A:ASP710 2.2 28.3 1.0 NE2 A:HIS709 2.2 25.6 1.0 O A:HOH1262 2.9 47.6 1.0 CG A:ASP822 3.0 27.9 1.0 CD2 A:HIS709 3.1 25.2 1.0 CD2 A:HIS673 3.1 26.6 1.0 CE1 A:HIS673 3.2 24.7 1.0 CG A:ASP710 3.2 27.0 1.0 CE1 A:HIS709 3.3 26.8 1.0 OD2 A:ASP822 3.3 32.0 1.0 OD1 A:ASP710 3.6 26.4 1.0 MG A:MG1003 3.8 12.2 1.0 O A:HOH1222 4.2 50.1 1.0 ND1 A:HIS673 4.3 23.2 1.0 CD2 A:HIS669 4.3 28.2 1.0 CG A:HIS709 4.3 27.2 1.0 CG A:HIS673 4.3 26.5 1.0 O A:HOH1276 4.3 39.8 1.0 ND1 A:HIS709 4.3 25.1 1.0 CB A:ASP822 4.4 29.1 1.0 CB A:ASP710 4.5 26.6 1.0 NE2 A:HIS669 4.5 25.8 1.0 CA A:ASP822 4.9 26.4 1.0 CG2 A:VAL677 5.0 23.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617


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-617 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:31.5 occ:1.00 OD1 B:ASP822 2.2 26.8 1.0 OD2 B:ASP710 2.2 28.7 1.0 NE2 B:HIS673 2.2 24.2 1.0 O B:HOH1171 2.3 28.2 1.0 NE2 B:HIS709 2.3 24.4 1.0 O B:HOH1197 2.4 29.6 1.0 CG B:ASP822 3.0 28.2 1.0 CE1 B:HIS673 3.1 23.9 1.0 CD2 B:HIS709 3.2 22.2 1.0 CG B:ASP710 3.2 26.2 1.0 CD2 B:HIS673 3.2 22.9 1.0 OD2 B:ASP822 3.3 32.2 1.0 CE1 B:HIS709 3.4 23.6 1.0 OD1 B:ASP710 3.5 22.4 1.0 MG B:MG1003 3.8 11.4 1.0 O B:HOH1244 4.1 29.0 1.0 CD2 B:HIS669 4.2 30.9 1.0 ND1 B:HIS673 4.3 25.0 1.0 CG B:HIS673 4.3 25.5 1.0 CG B:HIS709 4.4 22.1 1.0 ND1 B:HIS709 4.4 23.3 1.0 CB B:ASP822 4.4 25.8 1.0 NE2 B:HIS669 4.5 29.0 1.0 CB B:ASP710 4.5 23.7 1.0 CA B:ASP822 4.9 25.3 1.0

A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-617 To Be Published.