Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 13E, PDB code: 5h2q:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn1001 b:17.1 occ:1.00 OD2 A:ASP710 2.1 12.7 1.0 NE2 A:HIS673 2.1 13.3 1.0 NE2 A:HIS709 2.1 11.6 1.0 OD1 A:ASP823 2.2 13.8 1.0 O A:HOH1199 2.2 15.7 1.0 O A:HOH1101 2.3 13.3 1.0 CD2 A:HIS709 3.0 11.8 1.0 CG A:ASP823 3.1 16.5 1.0 CD2 A:HIS673 3.1 14.3 1.0 CG A:ASP710 3.1 13.4 1.0 CE1 A:HIS709 3.1 12.3 1.0 CE1 A:HIS673 3.1 12.7 1.0 OD2 A:ASP823 3.3 16.7 1.0 OD1 A:ASP710 3.6 12.7 1.0 MG A:MG1002 3.9 15.5 1.0 O A:HOH1291 4.1 14.9 1.0 CD2 A:HIS669 4.1 16.3 1.0 CG A:HIS709 4.2 12.0 1.0 O A:HOH1152 4.2 14.2 1.0 NE2 A:HIS669 4.2 15.8 1.0 CG A:HIS673 4.2 13.1 1.0 ND1 A:HIS709 4.2 13.1 1.0 ND1 A:HIS673 4.3 14.2 1.0 CB A:ASP710 4.4 9.9 1.0 CB A:ASP823 4.5 15.0 1.0 O A:HOH1106 4.8 13.0 1.0 CG2 A:VAL677 4.9 12.8 1.0 CA A:ASP823 4.9 14.2 1.0 C19 A:LLI1003 4.9 16.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1001 b:18.8 occ:1.00 OD2 B:ASP710 2.1 15.7 1.0 OD1 B:ASP823 2.1 13.7 1.0 NE2 B:HIS709 2.1 16.6 1.0 NE2 B:HIS673 2.2 14.9 1.0 O B:HOH1108 2.2 15.3 1.0 O B:HOH1102 2.4 15.8 1.0 CG B:ASP823 3.0 15.7 1.0 CD2 B:HIS709 3.1 17.1 1.0 CE1 B:HIS709 3.1 15.6 1.0 CD2 B:HIS673 3.2 15.6 1.0 CG B:ASP710 3.2 17.3 1.0 CE1 B:HIS673 3.2 15.2 1.0 OD2 B:ASP823 3.3 16.9 1.0 OD1 B:ASP710 3.7 14.7 1.0 MG B:MG1002 4.0 15.5 1.0 NE2 B:HIS669 4.1 17.7 1.0 CD2 B:HIS669 4.1 17.8 1.0 CG B:HIS709 4.2 15.2 1.0 O B:HOH1267 4.2 16.2 1.0 O B:HOH1158 4.2 12.9 1.0 ND1 B:HIS709 4.2 16.6 1.0 CG B:HIS673 4.3 14.8 1.0 ND1 B:HIS673 4.3 15.8 1.0 CB B:ASP710 4.4 13.3 1.0 CB B:ASP823 4.4 16.8 1.0 CG2 B:VAL677 4.7 18.4 1.0 O B:HOH1106 4.8 14.3 1.0 C19 B:LLI1003 4.8 16.2 1.0 CA B:ASP823 4.9 14.3 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.