Zinc in PDB 3l8e: Crystal Structure of Apo Form of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli

The structure of Crystal Structure of Apo Form of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli, PDB code: 3l8e was solved by H.Nguyen, E.Peisach, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.11 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.766, 63.967, 103.196, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.2

The binding sites of Zinc atom in the Crystal Structure of Apo Form of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli (pdb code 3l8e). 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 Apo Form of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli, PDB code: 3l8e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Apo Form of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli


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 Apo Form of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:12.4 occ:1.00 ND1 A:HIS94 2.2 10.7 1.0 SG A:CYS92 2.3 10.6 1.0 SG A:CYS109 2.3 13.3 1.0 SG A:CYS107 2.3 11.7 1.0 CE1 A:HIS94 3.1 13.1 1.0 CG A:HIS94 3.2 13.3 1.0 CB A:CYS107 3.3 15.3 1.0 CB A:CYS92 3.3 8.2 1.0 CB A:HIS94 3.5 10.6 1.0 CB A:CYS109 3.5 11.9 1.0 N A:ARG110 3.5 11.1 1.0 C A:CYS109 3.7 11.2 1.0 CA A:CYS109 3.8 12.3 1.0 N A:CYS109 3.9 13.4 1.0 CA A:CYS92 4.0 7.7 1.0 N A:HIS94 4.2 10.2 1.0 CB A:ARG110 4.3 11.6 1.0 CA A:ARG110 4.3 10.1 1.0 NE2 A:HIS94 4.3 12.2 1.0 CD2 A:HIS94 4.3 14.6 1.0 CA A:HIS94 4.4 11.4 1.0 CD A:PRO93 4.5 9.2 1.0 O A:HOH263 4.5 24.6 1.0 O A:CYS109 4.5 10.6 1.0 C A:CYS92 4.5 7.3 1.0 N A:PRO93 4.6 9.2 1.0 CA A:CYS107 4.7 15.3 1.0 O A:HOH204 4.8 12.6 1.0 N A:ASP108 5.0 14.8 1.0 C A:CYS107 5.0 14.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Apo Form of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli


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 Apo Form of D,D-Heptose 1.7-Bisphosphate Phosphatase From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:12.9 occ:1.00 ND1 B:HIS94 2.2 16.1 1.0 SG B:CYS92 2.3 10.5 1.0 SG B:CYS109 2.3 14.2 1.0 SG B:CYS107 2.4 12.0 1.0 CE1 B:HIS94 3.1 15.1 1.0 CG B:HIS94 3.2 16.4 1.0 CB B:CYS107 3.2 10.8 1.0 CB B:CYS92 3.4 10.8 1.0 CB B:CYS109 3.5 13.6 1.0 CB B:HIS94 3.5 11.7 1.0 N B:ARG110 3.5 10.8 1.0 C B:CYS109 3.7 11.1 1.0 CA B:CYS109 3.9 11.5 1.0 CA B:CYS92 3.9 10.9 1.0 N B:CYS109 4.0 14.0 1.0 N B:HIS94 4.2 10.0 1.0 NE2 B:HIS94 4.3 16.1 1.0 CA B:ARG110 4.3 8.6 1.0 CD2 B:HIS94 4.3 15.0 1.0 CB B:ARG110 4.3 10.8 1.0 O B:HOH213 4.4 18.7 1.0 O B:CYS109 4.4 10.5 1.0 CA B:HIS94 4.5 12.0 1.0 C B:CYS92 4.5 10.5 1.0 CD B:PRO93 4.6 13.6 1.0 N B:PRO93 4.6 10.8 1.0 CA B:CYS107 4.7 10.9 1.0 O B:HOH200 4.9 13.1 1.0

H.H.Nguyen, L.Wang, H.Huang, E.Peisach, D.Dunaway-Mariano, K.N.Allen. Structural Determinants of Substrate Recognition in the Had Superfamily Member D-Glycero-D-Manno-Heptose-1,7-Bisphosphate Phosphatase (Gmhb) . Biochemistry V. 49 1082 2010.
ISSN: ISSN 0006-2960
PubMed: 20050614
DOI: 10.1021/BI902019Q