Zinc in PDB 8xkf: Crystal Structure of Helicobacter Pylori Ispdf with Substrate Ctp

All present enzymatic activity of Crystal Structure of Helicobacter Pylori Ispdf with Substrate Ctp:
2.7.7.60; 4.6.1.12;

The structure of Crystal Structure of Helicobacter Pylori Ispdf with Substrate Ctp, PDB code: 8xkf was solved by X.Chen, D.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.56 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.624, 146.624, 256.495, 90, 90, 120
R / Rfree (%)	19.2 / 22.7

The structure of Crystal Structure of Helicobacter Pylori Ispdf with Substrate Ctp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Helicobacter Pylori Ispdf with Substrate Ctp (pdb code 8xkf). 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 Helicobacter Pylori Ispdf with Substrate Ctp, PDB code: 8xkf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Helicobacter Pylori Ispdf with Substrate Ctp


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 Helicobacter Pylori Ispdf with Substrate Ctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:84.5 occ:1.00 O1B C:CDP502 2.2 50.8 1.0 O3B C:CDP502 2.2 62.4 1.0 ND1 A:HIS288 2.3 34.0 1.0 PB C:CDP502 2.5 79.3 1.0 CE1 A:HIS288 2.6 35.8 1.0 NE2 A:HIS256 3.0 35.0 1.0 OD1 A:ASP254 3.0 34.0 1.0 O2B C:CDP502 3.1 65.9 1.0 CE1 A:HIS256 3.2 34.0 1.0 OD2 A:ASP254 3.6 30.0 1.0 CG A:ASP254 3.7 29.2 1.0 CG A:HIS288 3.7 32.7 1.0 O C:HOH639 3.8 37.2 1.0 NE2 A:HIS288 3.9 39.7 1.0 O3A C:CDP502 4.1 64.5 1.0 CD2 A:HIS256 4.2 29.5 1.0 ND1 A:HIS256 4.4 32.0 1.0 CD2 A:HIS288 4.4 37.9 1.0 CB A:HIS288 4.5 26.6 1.0 O C:HOH617 4.6 40.4 1.0 O A:HOH684 4.8 32.4 1.0 CG A:HIS256 5.0 30.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Helicobacter Pylori Ispdf with Substrate Ctp


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 Helicobacter Pylori Ispdf with Substrate Ctp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn505 b:86.6 occ:1.00 OD2 D:ASP254 2.2 35.9 1.0 NE2 D:HIS256 2.3 38.2 1.0 ND1 D:HIS288 2.3 38.8 1.0 O E:HOH604 2.7 49.1 1.0 CG D:ASP254 2.8 30.6 1.0 OD1 D:ASP254 2.9 32.9 1.0 CE1 D:HIS256 3.1 38.1 1.0 CG D:HIS288 3.1 32.0 1.0 CE1 D:HIS288 3.2 39.9 1.0 CD2 D:HIS256 3.4 32.4 1.0 CB D:HIS288 3.4 26.8 1.0 O3B E:CDP503 3.9 62.0 1.0 CD2 D:HIS288 4.1 31.4 1.0 NE2 D:HIS288 4.2 32.7 1.0 CB D:ASP254 4.2 25.6 1.0 ND1 D:HIS256 4.2 37.1 1.0 CG D:HIS256 4.4 32.9 1.0 O D:ASP284 4.6 31.3 1.0 O2B E:CDP503 4.7 64.0 1.0 PB E:CDP503 4.8 79.8 1.0 CA D:ALA285 4.8 27.0 1.0 CA D:HIS288 4.9 25.0 1.0 O E:HOH641 5.0 38.9 1.0

X.Chen, H.Zhao, C.Wang, M.Hamed, Q.Shang, Y.Yang, X.Diao, X.Sun, W.Hu, X.Jiang, Y.Zhang, A.K.H.Hirsch, D.Wu, J.Zhuang. Two Natural Compounds As Potential Inhibitors Against the Helicobacter Pylori and Acinetobacter Baumannii Ispd Enzymes. Int J Antimicrob Agents 07160 2024.
ISSN: ISSN 1872-7913
PubMed: 38537721
DOI: 10.1016/J.IJANTIMICAG.2024.107160