Magnesium in PDB 5h2q: Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E

The structure of Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E, PDB code: 5h2q was solved by C.G.Noble, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.19 / 1.66
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.210, 97.210, 120.440, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 20

The structure of Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E (pdb code 5h2q). 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 T Brucei Phosphodiesterase B2 Bound to Compound 13E, PDB code: 5h2q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E


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 T Brucei Phosphodiesterase B2 Bound to Compound 13E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:15.5 occ:1.00 O A:HOH1291 2.1 14.9 1.0 OD1 A:ASP710 2.1 12.7 1.0 O A:HOH1101 2.1 13.3 1.0 O A:HOH1122 2.1 16.0 1.0 O A:HOH1116 2.2 15.7 1.0 O A:HOH1106 2.2 13.0 1.0 CG A:ASP710 3.1 13.4 1.0 OD2 A:ASP710 3.5 12.7 1.0 ZN A:ZN1001 3.9 17.1 1.0 NE2 A:HIS745 4.0 12.5 1.0 OE2 A:GLU742 4.0 17.1 1.0 O A:HOH1199 4.1 15.7 1.0 O A:HIS709 4.2 14.3 1.0 OG1 A:THR783 4.2 13.2 1.0 O A:HOH1303 4.3 17.0 1.0 CD2 A:HIS709 4.3 11.8 1.0 CD2 A:HIS745 4.3 13.5 1.0 OD2 A:ASP823 4.4 16.7 1.0 CB A:ASP710 4.4 9.9 1.0 CD2 A:HIS713 4.5 16.1 1.0 O A:HOH1104 4.5 28.7 1.0 C19 A:LLI1003 4.5 16.5 1.0 NE2 A:HIS669 4.6 15.8 1.0 C18 A:LLI1003 4.6 20.0 1.0 CB A:THR783 4.7 15.4 1.0 NE2 A:HIS709 4.7 11.6 1.0 NE2 A:HIS713 4.8 15.8 1.0 CA A:ASP710 4.8 9.7 1.0 CD2 A:HIS669 4.8 16.3 1.0 O A:THR783 4.8 16.9 1.0 CD A:GLU742 4.9 18.0 1.0 O A:HOH1175 4.9 20.7 1.0 CG A:GLU742 5.0 14.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E


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 T Brucei Phosphodiesterase B2 Bound to Compound 13E within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:15.5 occ:1.00 OD1 B:ASP710 2.0 14.7 1.0 O B:HOH1106 2.1 14.3 1.0 O B:HOH1102 2.1 15.8 1.0 O B:HOH1267 2.1 16.2 1.0 O B:HOH1155 2.1 14.2 1.0 O B:HOH1137 2.1 13.8 1.0 CG B:ASP710 3.1 17.3 1.0 OD2 B:ASP710 3.5 15.7 1.0 NE2 B:HIS745 4.0 17.2 1.0 ZN B:ZN1001 4.0 18.8 1.0 OE2 B:GLU742 4.1 17.0 1.0 O B:HIS709 4.1 15.7 1.0 OG1 B:THR783 4.1 14.4 1.0 O B:HOH1108 4.2 15.3 1.0 CD2 B:HIS709 4.3 17.1 1.0 CD2 B:HIS745 4.3 17.4 1.0 O B:HOH1250 4.3 13.8 1.0 CB B:ASP710 4.4 13.3 1.0 O B:HOH1113 4.4 26.4 1.0 OD2 B:ASP823 4.4 16.9 1.0 CD2 B:HIS713 4.6 16.5 1.0 NE2 B:HIS669 4.6 17.7 1.0 C19 B:LLI1003 4.6 16.2 1.0 NE2 B:HIS709 4.7 16.6 1.0 C18 B:LLI1003 4.7 15.1 1.0 CB B:THR783 4.7 19.1 1.0 CA B:ASP710 4.8 13.4 1.0 CD2 B:HIS669 4.9 17.8 1.0 NE2 B:HIS713 4.9 15.5 1.0 O B:HOH1245 4.9 17.0 1.0 CD B:GLU742 4.9 20.6 1.0 O B:THR783 4.9 14.0 1.0 CG B:GLU742 4.9 17.6 1.0 C B:HIS709 5.0 18.0 1.0

P.S.Ng, C.G.Noble, F.S.B.Ng, S.H.Chew, C.C.Lim, V.Manoharan, K.F.Wan, P.Vachaspati, M.Kaiser, N.L.Ma, P.Gedeck, C.Kounde, S.P.S.Rao. Trypanosomal Phosphodiesterase B1 and B2 As A Potential Therapy For Human African Trypanosomiasis To Be Published.