Cobalt in PDB 2ew5: Structure of Helicobacter Pylori Peptide Deformylase in Complex with Inhibitor

All present enzymatic activity of Structure of Helicobacter Pylori Peptide Deformylase in Complex with Inhibitor:
3.5.1.88;

The structure of Structure of Helicobacter Pylori Peptide Deformylase in Complex with Inhibitor, PDB code: 2ew5 was solved by J.Cai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.117, 52.970, 92.259, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.4

The binding sites of Cobalt atom in the Structure of Helicobacter Pylori Peptide Deformylase in Complex with Inhibitor (pdb code 2ew5). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total only one binding site of Cobalt was determined in the Structure of Helicobacter Pylori Peptide Deformylase in Complex with Inhibitor, PDB code: 2ew5:

Cobalt binding site 1 out of 1 in the Structure of Helicobacter Pylori Peptide Deformylase in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Helicobacter Pylori Peptide Deformylase in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Co300 b:13.8 occ:1.00 O A:HOH424 2.0 6.0 1.0 NE2 A:HIS142 2.2 10.8 1.0 NE2 A:HIS138 2.2 9.9 1.0 SG A:CYS96 2.4 13.6 1.0 CD2 A:HIS138 2.9 9.4 1.0 CD2 A:HIS142 3.0 9.7 1.0 CE1 A:HIS142 3.3 9.3 1.0 CE1 A:HIS138 3.4 8.7 1.0 NE2 A:GLN51 3.4 8.3 1.0 O A:HOH309 3.5 7.5 1.0 CB A:CYS96 3.5 11.6 1.0 O A:HOH392 3.6 12.6 1.0 OE1 A:GLN51 3.8 8.7 1.0 CD A:GLN51 3.8 10.1 1.0 OE2 A:GLU139 3.9 12.2 1.0 CA A:CYS96 4.1 13.0 1.0 CG A:HIS142 4.2 10.0 1.0 CG A:HIS138 4.2 9.3 1.0 ND1 A:HIS142 4.3 10.9 1.0 ND1 A:HIS138 4.4 6.0 1.0 OE1 A:GLU139 4.4 10.2 1.0 O A:HOH305 4.5 6.6 1.0 CD A:GLU139 4.5 11.9 1.0 C7 A:Y12200 4.7 24.6 1.0 N A:LEU97 4.7 12.6 1.0 O A:GLY95 4.8 11.5 1.0 C A:CYS96 4.8 14.7 1.0 N9 A:Y12200 4.9 21.1 1.0 C8 A:Y12200 4.9 23.3 1.0

J.Cai, C.Han, T.Hu, J.Zhang, D.Wu, F.Wang, Y.Liu, J.Ding, K.Chen, J.Yue, X.Shen, H.Jiang. Peptide Deformylase Is A Potential Target For Anti-Helicobacter Pylori Drugs: Reverse Docking, Enzymatic Assay, and X-Ray Crystallography Validation Protein Sci. V. 15 2071 2006.
ISSN: ISSN 0961-8368
PubMed: 16882991
DOI: 10.1110/PS.062238406