Zinc in PDB 6qgu: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1361

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1361, PDB code: 6qgu 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)	57.40 / 1.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.467, 114.814, 68.314, 90.00, 108.23, 90.00
R / Rfree (%)	15.9 / 19.5

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1361 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-1361 (pdb code 6qgu). 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-1361, PDB code: 6qgu:
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-1361


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-1361 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:25.7 occ:1.00 NE2 A:HIS673 2.1 19.3 1.0 OD1 A:ASP822 2.1 20.4 1.0 O A:HOH1143 2.1 24.9 1.0 OD2 A:ASP710 2.2 22.6 1.0 NE2 A:HIS709 2.2 19.5 1.0 O A:HOH1210 2.3 28.2 1.0 CG A:ASP822 3.0 24.3 1.0 CD2 A:HIS673 3.1 21.8 1.0 CD2 A:HIS709 3.1 20.2 1.0 CG A:ASP710 3.1 20.6 1.0 CE1 A:HIS673 3.2 20.8 1.0 CE1 A:HIS709 3.2 21.1 1.0 OD2 A:ASP822 3.2 29.9 1.0 OD1 A:ASP710 3.5 20.4 1.0 MG A:MG1002 3.7 15.6 1.0 O A:HOH1292 4.1 52.6 1.0 CD2 A:HIS669 4.2 26.4 1.0 CG A:HIS673 4.2 21.9 1.0 CG A:HIS709 4.2 20.7 1.0 ND1 A:HIS673 4.3 21.5 1.0 O A:HOH1283 4.3 28.4 1.0 ND1 A:HIS709 4.3 19.8 1.0 CB A:ASP822 4.4 24.5 1.0 CB A:ASP710 4.4 21.7 1.0 NE2 A:HIS669 4.4 25.4 1.0 CA A:ASP822 4.9 22.3 1.0 CG2 A:VAL677 4.9 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-1361


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-1361 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:26.8 occ:1.00 NE2 B:HIS673 2.1 21.1 1.0 NE2 B:HIS709 2.1 21.9 1.0 OD1 B:ASP822 2.2 24.2 1.0 O B:HOH1130 2.2 26.1 1.0 OD2 B:ASP710 2.2 22.2 1.0 O B:HOH1228 2.3 28.8 1.0 CG B:ASP822 3.0 25.6 1.0 CD2 B:HIS709 3.0 20.4 1.0 CD2 B:HIS673 3.1 22.2 1.0 CE1 B:HIS673 3.1 22.5 1.0 CG B:ASP710 3.1 22.5 1.0 CE1 B:HIS709 3.2 21.1 1.0 OD2 B:ASP822 3.3 31.7 1.0 OD1 B:ASP710 3.5 20.8 1.0 MG B:MG1002 3.7 15.9 1.0 O B:HOH1237 4.1 28.9 1.0 O B:HOH1187 4.1 50.5 1.0 CG B:HIS709 4.2 20.7 1.0 CD2 B:HIS669 4.2 26.4 1.0 ND1 B:HIS673 4.2 21.9 1.0 CG B:HIS673 4.2 20.7 1.0 ND1 B:HIS709 4.2 20.8 1.0 CB B:ASP710 4.4 21.6 1.0 CB B:ASP822 4.4 24.7 1.0 NE2 B:HIS669 4.6 25.2 1.0 O B:HOH1165 4.7 23.6 1.0 CA B:ASP822 4.9 24.2 1.0 CG2 B:VAL677 4.9 22.4 1.0 O B:HOH1290 4.9 41.3 1.0

A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1361 To Be Published.