Zinc in PDB 2r8q: Structure of LMJPDEB1 in Complex with Ibmx

All present enzymatic activity of Structure of LMJPDEB1 in Complex with Ibmx:
3.1.4.17;

The structure of Structure of LMJPDEB1 in Complex with Ibmx, PDB code: 2r8q was solved by H.Wang, Z.Yan, J.Geng, S.Kunz, T.Seebeck, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.753, 78.688, 70.511, 90.00, 92.46, 90.00
R / Rfree (%)	19 / 20.8

The structure of Structure of LMJPDEB1 in Complex with Ibmx also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Structure of LMJPDEB1 in Complex with Ibmx (pdb code 2r8q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of LMJPDEB1 in Complex with Ibmx, PDB code: 2r8q:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of LMJPDEB1 in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of LMJPDEB1 in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:17.0 occ:1.00 OD2 A:ASP722 2.1 12.1 1.0 O A:HOH941 2.2 17.6 1.0 NE2 A:HIS685 2.2 14.7 1.0 OD1 A:ASP835 2.2 15.3 1.0 NE2 A:HIS721 2.2 15.1 1.0 O A:HOH942 2.3 18.7 1.0 CD2 A:HIS721 3.1 14.1 1.0 CG A:ASP835 3.1 16.8 1.0 CD2 A:HIS685 3.1 13.4 1.0 CG A:ASP722 3.2 14.6 1.0 CE1 A:HIS685 3.2 13.2 1.0 CE1 A:HIS721 3.3 15.3 1.0 OD2 A:ASP835 3.3 21.5 1.0 OD1 A:ASP722 3.7 14.4 1.0 MG A:MG2 3.8 15.9 1.0 O A:HOH946 4.1 15.8 1.0 CD2 A:HIS681 4.2 14.9 1.0 CG A:HIS721 4.2 14.0 1.0 NE2 A:HIS681 4.3 14.9 1.0 O A:HOH998 4.3 25.2 1.0 ND1 A:HIS685 4.3 12.8 1.0 ND1 A:HIS721 4.3 14.1 1.0 CG A:HIS685 4.3 12.3 1.0 CB A:ASP722 4.4 13.6 1.0 CB A:ASP835 4.5 16.0 1.0 O A:HOH945 4.7 14.6 1.0 O A:HOH949 4.8 36.5 1.0 CG2 A:VAL689 4.9 14.9 1.0 CA A:ASP835 4.9 15.7 1.0

Zinc binding site 2 out of 2 in the Structure of LMJPDEB1 in Complex with Ibmx


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of LMJPDEB1 in Complex with Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:17.0 occ:1.00 O B:HOH942 2.2 15.9 1.0 OD2 B:ASP722 2.2 14.3 1.0 NE2 B:HIS721 2.2 13.3 1.0 OD1 B:ASP835 2.2 16.0 1.0 NE2 B:HIS685 2.2 12.4 1.0 O B:HOH943 2.3 18.0 1.0 CD2 B:HIS721 3.1 12.7 1.0 CG B:ASP835 3.1 19.1 1.0 CD2 B:HIS685 3.1 13.3 1.0 CG B:ASP722 3.2 16.0 1.0 CE1 B:HIS685 3.2 14.0 1.0 CE1 B:HIS721 3.2 12.7 1.0 OD2 B:ASP835 3.3 19.9 1.0 OD1 B:ASP722 3.6 14.5 1.0 MG B:MG2 3.8 14.2 1.0 O B:HOH947 4.1 16.9 1.0 CD2 B:HIS681 4.1 15.8 1.0 NE2 B:HIS681 4.2 16.0 1.0 CG B:HIS721 4.2 12.5 1.0 O B:HOH970 4.2 18.9 1.0 ND1 B:HIS721 4.3 13.3 1.0 CG B:HIS685 4.3 14.0 1.0 ND1 B:HIS685 4.3 14.2 1.0 CB B:ASP722 4.4 15.2 1.0 CB B:ASP835 4.5 16.6 1.0 O B:HOH1047 4.6 30.4 1.0 O B:HOH946 4.7 15.0 1.0 CG2 B:VAL689 4.9 14.9 1.0 CA B:ASP835 4.9 16.4 1.0

H.Wang, Z.Yan, J.Geng, S.Kunz, T.Seebeck, H.Ke. Crystal Structure of the Leishmania Major Phosphodiesterase LMJPDEB1 and Insight Into the Design of the Parasite-Selective Inhibitors. Mol.Microbiol. V. 66 1029 2007.
ISSN: ISSN 0950-382X
PubMed: 17944832
DOI: 10.1111/J.1365-2958.2007.05976.X