Zinc in PDB 7e65: The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3

The structure of The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3, PDB code: 7e65 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)	67.58 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.441, 91.037, 100.877, 90, 90, 90
R / Rfree (%)	20.7 / 27.8

The binding sites of Zinc atom in the The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3 (pdb code 7e65). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3, PDB code: 7e65:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:48.6 occ:1.00 NE2 A:HIS168 1.9 36.1 1.0 OD1 A:ASP172 2.1 29.5 1.0 ND1 A:HIS249 2.2 32.4 1.0 O9 A:HXO302 2.4 62.5 1.0 CG A:ASP172 2.8 31.0 1.0 OD2 A:ASP172 2.8 32.8 1.0 CD2 A:HIS168 2.8 36.6 1.0 O8 A:HXO302 2.9 78.3 1.0 CE1 A:HIS168 2.9 37.9 1.0 CE1 A:HIS249 3.0 30.6 1.0 CG A:HIS249 3.2 31.0 1.0 N4 A:HXO302 3.3 75.0 1.0 C12 A:HXO302 3.5 85.3 1.0 CB A:HIS249 3.6 31.8 1.0 CG A:HIS168 4.0 38.5 1.0 ND1 A:HIS168 4.0 37.9 1.0 NE2 A:HIS249 4.1 31.9 1.0 CD2 A:HIS249 4.2 31.5 1.0 CB A:ASP172 4.3 30.9 1.0 CA A:HIS249 4.3 30.6 1.0 N A:ASP172 4.5 30.9 1.0 C A:THR171 4.6 33.0 1.0 C A:GLY170 4.6 37.7 1.0 NE2 A:HIS216 4.7 30.7 1.0 O A:GLY170 4.7 38.7 1.0 N A:THR171 4.7 35.2 1.0 O A:HOH402 4.7 49.3 1.0 CA A:ASP172 4.8 31.8 1.0 O A:THR171 4.9 31.0 1.0 N A:GLY170 4.9 44.1 1.0 CA A:GLY170 5.0 40.0 1.0

Zinc binding site 2 out of 2 in the The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn300 b:42.6 occ:1.00 OD1 B:ASP172 1.9 33.7 1.0 NE2 B:HIS168 2.0 39.0 1.0 ND1 B:HIS249 2.2 28.7 1.0 O B:HOH430 2.3 29.5 1.0 CG B:ASP172 2.6 31.6 1.0 OD2 B:ASP172 2.7 30.8 1.0 CE1 B:HIS168 3.0 39.6 1.0 CD2 B:HIS168 3.0 37.8 1.0 CE1 B:HIS249 3.1 26.6 1.0 CG B:HIS249 3.1 28.1 1.0 CB B:HIS249 3.5 27.9 1.0 CB B:ASP172 4.1 31.0 1.0 ND1 B:HIS168 4.1 40.0 1.0 NE2 B:HIS249 4.1 27.8 1.0 CG B:HIS168 4.1 39.8 1.0 CA B:HIS249 4.2 28.1 1.0 CD2 B:HIS249 4.2 27.1 1.0 N B:ASP172 4.4 32.9 1.0 C B:THR171 4.5 34.2 1.0 CA B:ASP172 4.6 30.4 1.0 C B:GLY170 4.7 31.4 1.0 N B:THR171 4.7 31.4 1.0 O B:GLY170 4.8 32.7 1.0 O B:THR171 4.8 38.6 1.0 NE2 B:HIS216 4.8 28.3 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