Zinc in PDB 7e63: The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 2-1

The structure of The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 2-1, PDB code: 7e63 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)	67.48 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.872, 90.734, 100.946, 90, 90, 90
R / Rfree (%)	19.3 / 26.5

The binding sites of Zinc atom in the The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 2-1 (pdb code 7e63). 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 2-1, PDB code: 7e63:
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 2-1


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 2-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:43.1 occ:1.00 NE2 A:HIS168 1.8 35.4 1.0 OD1 A:ASP172 1.9 32.7 1.0 O A:HOH468 2.1 52.4 1.0 ND1 A:HIS249 2.2 29.3 1.0 CG A:ASP172 2.6 35.0 1.0 OD2 A:ASP172 2.7 34.9 1.0 CE1 A:HIS168 2.8 35.7 1.0 CD2 A:HIS168 2.9 35.7 1.0 CE1 A:HIS249 3.1 27.8 1.0 CG A:HIS249 3.2 30.1 1.0 CB A:HIS249 3.5 29.7 1.0 ND1 A:HIS168 3.9 36.2 1.0 CG A:HIS168 4.0 35.4 1.0 CB A:ASP172 4.1 34.9 1.0 NE2 A:HIS249 4.2 28.7 1.0 CD2 A:HIS249 4.3 30.4 1.0 CA A:HIS249 4.3 29.9 1.0 O A:HOH484 4.4 48.6 1.0 N A:ASP172 4.5 33.2 1.0 NE2 A:HIS216 4.5 30.8 1.0 C A:THR171 4.6 31.2 1.0 CA A:ASP172 4.7 33.8 1.0 C A:GLY170 4.8 34.7 1.0 O A:GLY170 4.8 38.2 1.0 N A:THR171 4.9 30.7 1.0 O A:THR171 4.9 29.6 1.0 CD2 A:HIS216 5.0 30.1 1.0

Zinc binding site 2 out of 2 in the The Crystal Structure of Peptidoglycan Peptidase in Complex with Inhibitor 2-1


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 2-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:37.9 occ:1.00 OD1 B:ASP172 2.0 28.1 1.0 O9 B:HY9302 2.2 62.6 1.0 NE2 B:HIS168 2.2 38.9 1.0 ND1 B:HIS249 2.2 28.0 1.0 CG B:ASP172 2.7 28.5 1.0 OD2 B:ASP172 2.7 28.2 1.0 N4 B:HY9302 2.9 83.5 1.0 CD2 B:HIS168 3.1 36.7 1.0 CE1 B:HIS249 3.1 27.2 1.0 CE1 B:HIS168 3.3 37.9 1.0 CG B:HIS249 3.3 25.9 1.0 C12 B:HY9302 3.6 88.7 1.0 O8 B:HY9302 3.6 93.5 1.0 CB B:HIS249 3.7 25.2 1.0 CB B:ASP172 4.1 30.3 1.0 NE2 B:HIS249 4.3 27.3 1.0 CG B:HIS168 4.3 35.2 1.0 ND1 B:HIS168 4.3 36.0 1.0 CD2 B:HIS249 4.4 27.4 1.0 CA B:HIS249 4.5 25.3 1.0 N B:ASP172 4.5 30.0 1.0 C B:THR171 4.6 30.2 1.0 CA B:ASP172 4.7 31.0 1.0 C B:GLY170 4.8 30.9 1.0 N B:THR171 4.8 29.4 1.0 C5 B:HY9302 4.9 84.2 1.0 O B:THR171 4.9 30.2 1.0 O B:GLY170 4.9 30.7 1.0 NE2 B:HIS216 4.9 32.3 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