Zinc in PDB 4z1d: Structure of Pep and Zinc Bound KDO8PS From H.Pylori

All present enzymatic activity of Structure of Pep and Zinc Bound KDO8PS From H.Pylori:
2.5.1.55;

The structure of Structure of Pep and Zinc Bound KDO8PS From H.Pylori, PDB code: 4z1d was solved by B.J.Lee, S.Cho, H.Im, H.J.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.300, 51.013, 78.547, 90.00, 104.37, 90.00
R / Rfree (%)	18.6 / 21.2

The binding sites of Zinc atom in the Structure of Pep and Zinc Bound KDO8PS From H.Pylori (pdb code 4z1d). 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 Pep and Zinc Bound KDO8PS From H.Pylori, PDB code: 4z1d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Pep and Zinc Bound KDO8PS From H.Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Pep and Zinc Bound KDO8PS From H.Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.1 occ:1.00 OE1 A:GLU241 1.9 16.7 1.0 OD2 A:ASP252 2.0 22.1 1.0 NE2 A:HIS204 2.1 15.1 1.0 SG A:CYS18 2.3 16.2 1.0 CD A:GLU241 2.6 16.7 1.0 OE2 A:GLU241 2.8 16.9 1.0 CG A:ASP252 3.1 22.6 1.0 CE1 A:HIS204 3.1 15.3 1.0 CD2 A:HIS204 3.1 15.5 1.0 CB A:CYS18 3.2 14.9 1.0 O A:HOH562 3.4 26.1 1.0 CB A:ASP252 3.5 21.0 1.0 CA A:CYS18 4.0 14.4 1.0 O A:HOH631 4.0 39.5 1.0 CG A:GLU241 4.1 16.2 1.0 OD1 A:ASP252 4.2 24.4 1.0 ND1 A:HIS204 4.2 15.2 1.0 CG A:HIS204 4.2 15.1 1.0 CG2 A:THR203 4.4 16.4 1.0 CB A:GLU241 4.7 15.7 1.0 NZ A:LYS52 4.7 18.4 1.0 NZ A:LYS47 4.8 15.9 1.0 O1 A:PEP300 4.8 18.0 1.0 CA A:ASP252 5.0 20.2 1.0 N A:CYS18 5.0 14.4 1.0

Zinc binding site 2 out of 2 in the Structure of Pep and Zinc Bound KDO8PS From H.Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Pep and Zinc Bound KDO8PS From H.Pylori within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:64.2 occ:1.00 OE1 B:GLU241 1.4 26.7 1.0 CD B:GLU241 2.5 25.5 1.0 OD2 B:ASP252 2.7 22.9 1.0 NE2 B:HIS204 2.9 14.2 1.0 CB B:GLU241 3.1 20.3 1.0 CG B:GLU241 3.2 22.6 1.0 CB B:CYS18 3.3 15.2 1.0 SG B:CYS18 3.3 14.9 1.0 CG2 B:THR203 3.4 14.8 1.0 CE1 B:HIS204 3.4 14.8 1.0 OE2 B:GLU241 3.5 31.2 1.0 CG B:ASP252 3.6 23.2 1.0 CA B:CYS18 3.7 14.6 1.0 CB B:ASP252 3.8 20.9 1.0 CD2 B:HIS204 3.9 14.8 1.0 N B:CYS18 4.3 13.9 1.0 CB B:THR203 4.3 14.6 1.0 CG B:MET256 4.4 17.7 1.0 ND1 B:HIS204 4.5 14.1 1.0 CA B:GLU241 4.6 17.9 1.0 OG1 B:THR203 4.7 14.9 1.0 CG B:HIS204 4.7 14.4 1.0 SD B:MET256 4.7 16.9 1.0 OD1 B:ASP252 4.7 24.2 1.0 NZ B:LYS47 4.9 16.6 1.0

S.Cho, H.Im, K.Y.Lee, J.Chen, H.J.Kang, H.J.Yoon, K.H.Min, K.R.Lee, H.J.Park, B.J.Lee. Identification of Novel Scaffolds For Potential Anti-Helicobacter Pylori Agents Based on the Crystal Structure of H. Pylori 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase (HPKDO8PS). Eur.J.Med.Chem. V. 108 188 2016.
ISSN: ISSN 0223-5234
PubMed: 26649906
DOI: 10.1016/J.EJMECH.2015.11.036