Zinc in PDB 7a2f: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656, PDB code: 7a2f 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)	79.38 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.58, 115, 68.45, 90, 108.36, 90
R / Rfree (%)	18.8 / 22.4

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656 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-656 (pdb code 7a2f). 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-656, PDB code: 7a2f:
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-656


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-656 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:24.4 occ:1.00 O A:HOH1203 1.8 33.5 1.0 OD1 A:ASP822 2.1 16.8 1.0 NE2 A:HIS673 2.1 18.5 1.0 NE2 A:HIS709 2.2 17.0 1.0 OD2 A:ASP710 2.2 21.6 1.0 O A:HOH1107 2.4 21.7 1.0 CG A:ASP822 3.0 19.2 1.0 CD2 A:HIS709 3.1 16.6 1.0 CD2 A:HIS673 3.1 19.2 1.0 CE1 A:HIS673 3.1 18.5 1.0 CG A:ASP710 3.2 20.4 1.0 CE1 A:HIS709 3.2 17.4 1.0 OD2 A:ASP822 3.2 18.6 1.0 OD1 A:ASP710 3.6 19.7 1.0 O A:HOH1211 3.7 33.8 1.0 MG A:MG1002 3.8 9.5 1.0 CD2 A:HIS669 4.1 22.2 1.0 O A:HOH1268 4.2 35.9 1.0 ND1 A:HIS673 4.2 19.5 1.0 CG A:HIS709 4.2 17.5 1.0 CG A:HIS673 4.2 19.7 1.0 ND1 A:HIS709 4.2 16.5 1.0 CB A:ASP822 4.3 18.9 1.0 CB A:ASP710 4.4 20.5 1.0 NE2 A:HIS669 4.5 20.7 1.0 CA A:ASP822 4.8 19.0 1.0 CG2 A:VAL677 4.9 16.8 1.0 O A:HOH1110 4.9 16.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656


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-656 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:24.6 occ:1.00 NE2 B:HIS673 2.1 18.2 1.0 O B:HOH1118 2.1 21.5 1.0 OD1 B:ASP822 2.1 22.1 1.0 NE2 B:HIS709 2.2 17.2 1.0 OD2 B:ASP710 2.2 16.8 1.0 O B:HOH1129 2.3 25.4 1.0 CG B:ASP822 3.0 24.5 1.0 CD2 B:HIS709 3.1 16.0 1.0 CE1 B:HIS673 3.1 18.5 1.0 CD2 B:HIS673 3.1 18.4 1.0 CG B:ASP710 3.1 16.4 1.0 CE1 B:HIS709 3.2 17.4 1.0 OD2 B:ASP822 3.3 29.3 1.0 OD1 B:ASP710 3.5 15.1 1.0 MG B:MG1003 3.8 7.8 1.0 O B:HOH1222 4.0 26.7 1.0 CD2 B:HIS669 4.1 22.5 1.0 ND1 B:HIS673 4.2 18.4 1.0 CG B:HIS709 4.2 16.7 1.0 CG B:HIS673 4.2 18.7 1.0 ND1 B:HIS709 4.3 16.6 1.0 CB B:ASP822 4.4 24.8 1.0 CB B:ASP710 4.4 16.2 1.0 NE2 B:HIS669 4.5 22.0 1.0 O B:HOH1152 4.7 19.5 1.0 CA B:ASP822 4.9 24.0 1.0 CG2 B:VAL677 4.9 20.0 1.0

A.K.Singh, D.G.Brown. Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-656 To Be Published.