Zinc in PDB 6fdx: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1086

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1086, PDB code: 6fdx 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)	57.10 / 2.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.102, 116.385, 68.310, 90.00, 108.67, 90.00
R / Rfree (%)	16.9 / 23.2

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1086 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-1086 (pdb code 6fdx). 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-1086, PDB code: 6fdx:
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-1086


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-1086 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:56.4 occ:1.00 NE2 A:HIS709 1.9 44.2 1.0 O A:HOH1109 1.9 55.6 1.0 OD2 A:ASP710 1.9 51.9 1.0 NE2 A:HIS673 2.1 54.2 1.0 OD1 A:ASP822 2.3 58.3 1.0 CE1 A:HIS709 2.7 50.5 1.0 O A:HOH1162 2.9 61.2 1.0 CD2 A:HIS709 2.9 47.6 1.0 CE1 A:HIS673 3.0 51.8 1.0 CG A:ASP710 3.0 50.6 1.0 CD2 A:HIS673 3.1 53.3 1.0 CG A:ASP822 3.2 59.9 1.0 OD2 A:ASP822 3.3 54.3 1.0 OD1 A:ASP710 3.5 49.4 1.0 O A:HOH1110 3.8 66.3 1.0 ND1 A:HIS709 3.9 44.7 1.0 MG A:MG1002 3.9 37.8 1.0 CG A:HIS709 4.0 47.6 1.0 ND1 A:HIS673 4.1 57.7 1.0 CG A:HIS673 4.2 53.9 1.0 CB A:ASP710 4.3 50.0 1.0 CD2 A:HIS669 4.4 55.3 1.0 O A:HOH1101 4.5 35.5 1.0 CB A:ASP822 4.6 63.5 1.0 NE2 A:HIS669 4.7 59.7 1.0 CG2 A:VAL677 4.9 44.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1086


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-1086 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:45.8 occ:1.00 OD2 B:ASP710 1.9 41.8 1.0 NE2 B:HIS709 2.2 35.8 1.0 OD1 B:ASP822 2.3 48.1 1.0 O B:HOH1146 2.3 32.0 1.0 NE2 B:HIS673 2.3 41.0 1.0 O B:HOH1106 2.5 37.8 1.0 CG B:ASP710 2.9 39.6 1.0 CD2 B:HIS709 3.0 36.7 1.0 CG B:ASP822 3.1 49.4 1.0 CD2 B:HIS673 3.1 42.2 1.0 OD2 B:ASP822 3.1 45.0 1.0 CE1 B:HIS709 3.2 39.8 1.0 CE1 B:HIS673 3.4 48.3 1.0 OD1 B:ASP710 3.4 41.0 1.0 MG B:MG1002 3.8 25.0 1.0 O B:HOH1156 3.9 41.8 1.0 CB B:ASP710 4.1 38.9 1.0 CG B:HIS709 4.2 32.6 1.0 CD2 B:HIS669 4.2 47.6 1.0 ND1 B:HIS709 4.3 33.3 1.0 CG B:HIS673 4.3 46.9 1.0 ND1 B:HIS673 4.5 48.1 1.0 CB B:ASP822 4.5 51.8 1.0 NE2 B:HIS669 4.5 50.1 1.0 O B:HOH1110 4.5 32.8 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-1086 To Be Published.