Zinc in PDB 4i15: Crystal Structure of TBRPDEB1

The structure of Crystal Structure of TBRPDEB1, PDB code: 4i15 was solved by H.Wang, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.007, 115.337, 68.506, 90.00, 108.13, 90.00
R / Rfree (%)	20.4 / 22.3

The structure of Crystal Structure of TBRPDEB1 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of TBRPDEB1 (pdb code 4i15). 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 TBRPDEB1, PDB code: 4i15:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of TBRPDEB1


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 TBRPDEB1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:26.8 occ:1.00 OD2 A:ASP710 2.1 22.8 1.0 OD1 A:ASP822 2.1 21.2 1.0 O A:HOH1101 2.1 24.0 1.0 NE2 A:HIS709 2.2 20.8 1.0 NE2 A:HIS673 2.2 23.5 1.0 O A:HOH1102 2.5 29.2 1.0 CG A:ASP822 3.0 22.8 1.0 CD2 A:HIS709 3.1 22.4 1.0 CD2 A:HIS673 3.1 22.4 1.0 CG A:ASP710 3.1 22.6 1.0 CE1 A:HIS709 3.2 22.3 1.0 CE1 A:HIS673 3.2 21.6 1.0 OD2 A:ASP822 3.3 25.8 1.0 OD1 A:ASP710 3.6 21.2 1.0 MG A:MG1002 3.8 26.3 1.0 CD2 A:HIS669 4.1 24.8 1.0 O A:HOH1106 4.1 28.6 1.0 CG A:HIS709 4.2 20.5 1.0 ND1 A:HIS709 4.3 23.2 1.0 CG A:HIS673 4.3 22.3 1.0 ND1 A:HIS673 4.3 23.5 1.0 NE2 A:HIS669 4.3 26.2 1.0 CB A:ASP710 4.4 22.1 1.0 CB A:ASP822 4.4 21.6 1.0 O A:HOH1342 4.5 53.3 1.0 O A:HOH1105 4.9 19.9 1.0 CA A:ASP822 4.9 20.4 1.0 CG2 A:VAL677 4.9 19.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of TBRPDEB1


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 TBRPDEB1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:26.7 occ:1.00 OD2 B:ASP710 2.1 23.6 1.0 OD1 B:ASP822 2.1 23.5 1.0 NE2 B:HIS709 2.2 23.1 1.0 NE2 B:HIS673 2.2 23.3 1.0 O B:HOH1101 2.2 23.5 1.0 O B:HOH1102 2.4 26.9 1.0 CG B:ASP822 3.0 24.0 1.0 CD2 B:HIS709 3.0 21.9 1.0 CG B:ASP710 3.1 22.5 1.0 CD2 B:HIS673 3.1 22.5 1.0 CE1 B:HIS673 3.2 22.9 1.0 CE1 B:HIS709 3.2 21.7 1.0 OD2 B:ASP822 3.3 27.9 1.0 OD1 B:ASP710 3.6 22.4 1.0 MG B:MG1002 3.8 25.6 1.0 CD2 B:HIS669 4.1 23.4 1.0 O B:HOH1106 4.1 23.9 1.0 CG B:HIS709 4.2 21.6 1.0 ND1 B:HIS709 4.3 22.3 1.0 ND1 B:HIS673 4.3 22.7 1.0 CG B:HIS673 4.3 21.8 1.0 NE2 B:HIS669 4.3 24.3 1.0 CB B:ASP710 4.4 21.6 1.0 CB B:ASP822 4.4 21.8 1.0 O B:HOH1257 4.4 45.1 1.0 O B:HOH1105 4.9 23.1 1.0 CA B:ASP822 4.9 20.7 1.0 CG2 B:VAL677 4.9 22.3 1.0

C.Jansen, H.Wang, A.J.Kooistra, C.De Graaf, K.M.Orrling, H.Tenor, T.Seebeck, D.Bailey, I.J.De Esch, H.Ke, R.Leurs. Discovery of Novel Trypanosoma Brucei Phosphodiesterase B1 Inhibitors By Virtual Screening Against the Unliganded TBRPDEB1 Crystal Structure. J.Med.Chem. V. 56 2087 2013.
ISSN: ISSN 0022-2623
PubMed: 23409953
DOI: 10.1021/JM3017877