Zinc in PDB 5h2r: Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B

The structure of Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B, PDB code: 5h2r 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)	49.16 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.756, 97.756, 120.783, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 22.4

The structure of Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B 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 15B (pdb code 5h2r). 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 15B, PDB code: 5h2r:
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 15B


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 15B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:15.1 occ:1.00 OD2 A:ASP710 2.1 9.7 1.0 NE2 A:HIS709 2.1 8.4 1.0 NE2 A:HIS673 2.2 9.5 1.0 OD1 A:ASP823 2.2 12.1 1.0 O A:HOH1175 2.2 10.4 1.0 O A:HOH1102 2.3 10.7 1.0 CD2 A:HIS709 3.0 8.8 1.0 CG A:ASP823 3.1 12.3 1.0 CD2 A:HIS673 3.1 10.1 1.0 CG A:ASP710 3.1 8.5 1.0 CE1 A:HIS709 3.2 8.6 1.0 CE1 A:HIS673 3.2 8.4 1.0 OD2 A:ASP823 3.3 15.6 1.0 OD1 A:ASP710 3.6 8.7 1.0 MG A:MG1002 3.9 13.1 1.0 CD2 A:HIS669 4.1 15.4 1.0 O A:HOH1239 4.1 8.1 1.0 CG A:HIS709 4.2 8.3 1.0 O A:HOH1162 4.2 12.3 1.0 NE2 A:HIS669 4.2 14.9 1.0 ND1 A:HIS709 4.3 8.9 1.0 CG A:HIS673 4.3 8.7 1.0 ND1 A:HIS673 4.3 8.8 1.0 CB A:ASP710 4.4 6.7 1.0 CB A:ASP823 4.5 10.3 1.0 CG2 A:VAL677 4.9 12.1 1.0 O A:HOH1107 4.9 12.2 1.0 CA A:ASP823 4.9 9.3 1.0 C24 A:LLN1003 5.0 13.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of T Brucei Phosphodiesterase B2 Bound to Compound 15B


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 15B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:16.5 occ:1.00 OD1 B:ASP823 2.1 10.2 1.0 NE2 B:HIS709 2.1 13.6 1.0 NE2 B:HIS673 2.2 11.0 1.0 OD2 B:ASP710 2.2 13.1 1.0 O B:HOH1110 2.3 16.4 1.0 O B:HOH1101 2.5 11.8 1.0 CD2 B:HIS709 3.0 14.1 1.0 CG B:ASP823 3.1 11.6 1.0 CD2 B:HIS673 3.1 12.1 1.0 CE1 B:HIS709 3.2 13.9 1.0 CG B:ASP710 3.2 11.3 1.0 CE1 B:HIS673 3.2 11.2 1.0 OD2 B:ASP823 3.3 12.7 1.0 OD1 B:ASP710 3.7 12.7 1.0 MG B:MG1002 4.0 16.5 1.0 O B:HOH1113 4.1 12.3 1.0 O B:HOH1228 4.1 11.8 1.0 NE2 B:HIS669 4.1 15.1 1.0 CD2 B:HIS669 4.1 14.9 1.0 CG B:HIS709 4.2 13.6 1.0 CG B:HIS673 4.2 10.9 1.0 ND1 B:HIS709 4.3 15.1 1.0 ND1 B:HIS673 4.3 11.9 1.0 CB B:ASP710 4.4 11.3 1.0 CB B:ASP823 4.5 9.0 1.0 CG2 B:VAL677 4.7 13.3 1.0 CA B:ASP823 4.9 8.1 1.0 O B:HOH1103 4.9 7.8 1.0 C24 B:LLN1003 4.9 11.6 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.