Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of TBRPDEB1 (pdb code 4i15). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of TBRPDEB1, PDB code: 4i15:
Jump to Magnesium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of TBRPDEB1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:26.3 occ:1.00 OD1 A:ASP710 2.1 21.2 1.0 O A:HOH1101 2.2 24.0 1.0 O A:HOH1103 2.2 23.2 1.0 O A:HOH1105 2.2 19.9 1.0 O A:HOH1106 2.3 28.6 1.0 O A:HOH1104 2.3 24.2 1.0 CG A:ASP710 3.2 22.6 1.0 OD2 A:ASP710 3.5 22.8 1.0 ZN A:ZN1001 3.8 26.8 1.0 O A:HOH1102 4.1 29.2 1.0 O A:HIS709 4.1 20.6 1.0 NE2 A:HIS745 4.1 22.6 1.0 O A:HOH1302 4.2 51.7 1.0 CD2 A:HIS709 4.2 22.4 1.0 OG1 A:THR783 4.2 22.3 1.0 OE2 A:GLU742 4.3 26.5 1.0 OD2 A:ASP822 4.4 25.8 1.0 CD2 A:HIS745 4.5 21.4 1.0 O A:HOH1107 4.5 27.3 1.0 CB A:ASP710 4.5 22.1 1.0 CD2 A:HIS713 4.5 22.9 1.0 O A:HOH1151 4.5 29.4 1.0 NE2 A:HIS709 4.6 20.8 1.0 CD2 A:HIS669 4.7 24.8 1.0 CB A:THR783 4.7 21.6 1.0 NE2 A:HIS669 4.7 26.2 1.0 CA A:ASP710 4.8 21.5 1.0 NE2 A:HIS713 4.9 22.8 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of TBRPDEB1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:25.6 occ:1.00 OD1 B:ASP710 2.1 22.4 1.0 O B:HOH1101 2.2 23.5 1.0 O B:HOH1103 2.2 22.5 1.0 O B:HOH1106 2.2 23.9 1.0 O B:HOH1105 2.3 23.1 1.0 O B:HOH1104 2.3 23.1 1.0 CG B:ASP710 3.2 22.5 1.0 OD2 B:ASP710 3.5 23.6 1.0 ZN B:ZN1001 3.8 26.7 1.0 O B:HIS709 4.0 21.6 1.0 O B:HOH1102 4.1 26.9 1.0 NE2 B:HIS745 4.1 21.0 1.0 OE2 B:GLU742 4.2 27.4 1.0 OG1 B:THR783 4.2 25.6 1.0 CD2 B:HIS709 4.3 21.9 1.0 O B:HOH1107 4.3 25.9 1.0 O B:HOH1220 4.4 44.8 1.0 CD2 B:HIS745 4.4 19.9 1.0 OD2 B:ASP822 4.4 27.9 1.0 CB B:ASP710 4.5 21.6 1.0 CD2 B:HIS713 4.5 21.9 1.0 NE2 B:HIS709 4.7 23.1 1.0 CD2 B:HIS669 4.7 23.4 1.0 NE2 B:HIS669 4.7 24.3 1.0 CA B:ASP710 4.7 21.3 1.0 CB B:THR783 4.7 23.6 1.0 NE2 B:HIS713 4.8 20.6 1.0 C B:HIS709 4.9 20.8 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