Zinc in PDB 7e69: The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3-3

The structure of The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3-3, PDB code: 7e69 was solved by Y.Choi, K.J.Min, H.J.Yoon, H.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.38 / 2.61
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	115.649, 115.649, 56.614, 90, 90, 120
R / Rfree (%)	17 / 23.1

The binding sites of Zinc atom in the The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3-3 (pdb code 7e69). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3-3, PDB code: 7e69:

Zinc binding site 1 out of 1 in the The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3-3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:31.6 occ:1.00 ND1 A:HIS249 1.8 23.3 1.0 O18 A:HX6302 1.9 60.8 1.0 OD1 A:ASP172 2.0 23.2 1.0 NE2 A:HIS168 2.0 21.4 1.0 N13 A:HX6302 2.3 76.7 1.0 CE1 A:HIS249 2.5 23.1 1.0 CG A:ASP172 2.9 23.0 1.0 CE1 A:HIS168 2.9 22.9 1.0 CG A:HIS249 3.1 22.5 1.0 CD2 A:HIS168 3.1 21.2 1.0 OD2 A:ASP172 3.1 21.6 1.0 C72 A:HX6302 3.3 81.2 1.0 O16 A:HX6302 3.6 102.5 1.0 CB A:HIS249 3.7 21.7 1.0 NE2 A:HIS249 3.7 22.0 1.0 CD2 A:HIS249 4.0 21.7 1.0 ND1 A:HIS168 4.1 22.7 1.0 CG A:HIS168 4.2 22.7 1.0 CA A:HIS249 4.3 21.5 1.0 CB A:ASP172 4.4 22.5 1.0 C62 A:HX6302 4.4 72.7 1.0 C52 A:HX6302 4.5 80.4 1.0 N A:ASP172 4.6 19.6 1.0 C A:THR171 4.6 21.5 1.0 NH2 A:ARG242 4.7 42.7 1.0 C A:GLY170 4.8 21.5 1.0 CA A:ASP172 4.8 20.6 1.0 O A:THR171 4.8 24.3 1.0 O A:GLY170 4.8 21.4 1.0 N A:THR171 4.9 20.8 1.0

Y.Choi, J.S.Park, J.Kim, K.Min, K.Mahasenan, C.Kim, H.J.Yoon, S.Lim, D.H.Cheon, Y.Lee, S.Ryu, S.Mobashery, B.M.Kim, H.H.Lee. Structure-Based Inhibitor Design For Reshaping Bacterial Morphology Commun Biol V. 5 395 2022.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-022-03355-3