Cadmium in PDB 4z1c: Structure of Cadmium Bound KDO8PS From H.Pylori

All present enzymatic activity of Structure of Cadmium Bound KDO8PS From H.Pylori:
2.5.1.55;

The structure of Structure of Cadmium Bound KDO8PS From H.Pylori, PDB code: 4z1c 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)	28.97 / 1.93
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.353, 51.017, 78.667, 90.00, 104.70, 90.00
R / Rfree (%)	19.1 / 21.2

The binding sites of Cadmium atom in the Structure of Cadmium Bound KDO8PS From H.Pylori (pdb code 4z1c). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Structure of Cadmium Bound KDO8PS From H.Pylori, PDB code: 4z1c:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Structure of Cadmium Bound KDO8PS From H.Pylori


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Cadmium Bound KDO8PS From H.Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd300 b:22.2 occ:1.00 OE1 A:GLU241 2.3 17.9 1.0 O A:HOH542 2.3 21.8 1.0 NE2 A:HIS204 2.4 21.9 1.0 SG A:CYS18 2.6 17.0 1.0 OE2 A:GLU241 2.6 19.3 1.0 CD A:GLU241 2.8 17.2 1.0 OD2 A:ASP252 2.8 38.1 1.0 CG A:ASP252 3.3 35.0 1.0 CE1 A:HIS204 3.3 24.5 1.0 CD2 A:HIS204 3.4 24.3 1.0 CB A:CYS18 3.4 14.6 1.0 CB A:ASP252 3.6 30.0 1.0 CA A:CYS18 4.1 14.8 1.0 OD1 A:ASP252 4.2 44.9 1.0 NZ A:LYS52 4.2 23.4 1.0 CG A:GLU241 4.3 19.2 1.0 O A:HOH530 4.4 33.7 1.0 ND1 A:HIS204 4.5 22.7 1.0 CG A:HIS204 4.5 25.1 1.0 NZ A:LYS47 4.6 22.6 1.0 CG2 A:THR203 4.7 15.6 1.0 O A:HOH439 4.9 30.7 1.0 C A:CYS18 4.9 16.8 1.0 CE A:LYS52 4.9 24.4 1.0 CB A:GLU241 5.0 18.4 1.0

Cadmium binding site 2 out of 2 in the Structure of Cadmium Bound KDO8PS From H.Pylori


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Cadmium Bound KDO8PS From H.Pylori within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd300 b:23.3 occ:1.00 OE1 B:GLU241 2.3 13.1 1.0 NE2 B:HIS204 2.3 24.8 1.0 O B:HOH522 2.4 28.8 1.0 SG B:CYS18 2.6 19.5 1.0 OE2 B:GLU241 2.7 16.7 1.0 OD2 B:ASP252 2.7 33.3 1.0 CD B:GLU241 2.8 15.3 1.0 CD2 B:HIS204 3.3 26.7 1.0 CE1 B:HIS204 3.3 24.5 1.0 CB B:CYS18 3.3 20.6 1.0 CG B:ASP252 3.5 41.5 1.0 CB B:ASP252 3.8 35.0 1.0 CA B:CYS18 4.1 20.7 1.0 NZ B:LYS52 4.2 24.3 1.0 O B:HOH473 4.3 33.0 1.0 CG B:GLU241 4.3 17.3 1.0 O B:HOH551 4.4 35.7 1.0 NZ B:LYS47 4.4 20.5 1.0 CG B:HIS204 4.4 26.6 1.0 ND1 B:HIS204 4.4 27.9 1.0 OD1 B:ASP252 4.6 43.4 1.0 C B:CYS18 4.9 21.1 1.0 CE B:LYS52 5.0 28.2 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