Zinc in PDB 6fv9: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-007

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-007, PDB code: 6fv9 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)	79.47 / 2.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.203, 114.619, 68.387, 90.00, 108.36, 90.00
R / Rfree (%)	20.6 / 25.4

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-007 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-007 (pdb code 6fv9). 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-007, PDB code: 6fv9:
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-007


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-007 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:16.7 occ:1.00 OD1 A:ASP822 2.1 12.1 1.0 NE2 A:HIS673 2.1 11.8 1.0 OD2 A:ASP710 2.2 11.0 1.0 O A:HOH1159 2.2 10.6 1.0 O A:HOH1117 2.3 7.5 1.0 NE2 A:HIS709 2.3 11.7 1.0 CG A:ASP822 3.0 12.4 1.0 CD2 A:HIS673 3.1 12.0 1.0 CE1 A:HIS673 3.1 11.7 1.0 CD2 A:HIS709 3.1 11.6 1.0 CG A:ASP710 3.3 11.1 1.0 OD2 A:ASP822 3.3 12.2 1.0 CE1 A:HIS709 3.3 11.7 1.0 OD1 A:ASP710 3.6 10.4 1.0 MG A:MG1001 3.9 4.4 1.0 O A:HOH1206 4.0 23.0 1.0 O A:HOH1236 4.0 20.7 1.0 CD2 A:HIS669 4.1 13.7 1.0 NE2 A:HIS669 4.2 13.5 1.0 ND1 A:HIS673 4.2 12.1 1.0 CG A:HIS673 4.3 12.2 1.0 CG A:HIS709 4.3 11.7 1.0 ND1 A:HIS709 4.4 11.7 1.0 CB A:ASP822 4.4 12.3 1.0 CB A:ASP710 4.5 11.6 1.0 O A:HOH1144 4.7 6.8 1.0 CA A:ASP822 4.8 12.1 1.0 CG2 A:VAL677 4.8 11.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-007


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-007 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:24.4 occ:1.00 NE2 B:HIS673 2.1 15.2 1.0 OD2 B:ASP710 2.1 12.9 1.0 OD1 B:ASP822 2.2 18.2 1.0 O B:HOH1164 2.3 7.5 1.0 O B:HOH1121 2.3 8.7 1.0 NE2 B:HIS709 2.3 11.7 1.0 CE1 B:HIS673 2.9 14.8 1.0 CD2 B:HIS709 3.1 12.0 1.0 CG B:ASP822 3.2 18.0 1.0 CD2 B:HIS673 3.2 14.7 1.0 CG B:ASP710 3.2 13.0 1.0 CE1 B:HIS709 3.4 12.0 1.0 OD2 B:ASP822 3.5 17.9 1.0 OD1 B:ASP710 3.7 12.6 1.0 MG B:MG1001 3.9 5.2 1.0 CD2 B:HIS669 4.0 17.8 1.0 NE2 B:HIS669 4.1 18.0 1.0 ND1 B:HIS673 4.1 14.5 1.0 O B:HOH1194 4.1 17.6 1.0 CG B:HIS673 4.3 14.7 1.0 CG B:HIS709 4.3 12.0 1.0 ND1 B:HIS709 4.4 12.0 1.0 CB B:ASP710 4.5 13.2 1.0 CB B:ASP822 4.5 18.0 1.0 O B:HOH1137 4.7 7.2 1.0 O B:HOH1196 4.9 8.3 1.0 CA B:ASP822 4.9 17.6 1.0 CG2 B:VAL677 4.9 13.9 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-007 To Be Published.