Zinc in PDB 6jmy: Structure of Wild Type Closed Form of Peptidoglycan Peptidase

The structure of Structure of Wild Type Closed Form of Peptidoglycan Peptidase, PDB code: 6jmy was solved by K.J.Min, D.R.An, H.J.Yoon, S.W.Suh, H.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.95 / 1.66
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.891, 57.891, 152.708, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.6

The binding sites of Zinc atom in the Structure of Wild Type Closed Form of Peptidoglycan Peptidase (pdb code 6jmy). 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 Structure of Wild Type Closed Form of Peptidoglycan Peptidase, PDB code: 6jmy:

Zinc binding site 1 out of 1 in the Structure of Wild Type Closed Form of Peptidoglycan Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Wild Type Closed Form of Peptidoglycan Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.9 occ:1.00 OD1 A:ASP172 2.0 18.9 1.0 ND1 A:HIS249 2.0 21.5 1.0 O5 A:CIT302 2.0 26.7 1.0 NE2 A:HIS168 2.1 20.0 1.0 O6 A:CIT302 2.4 27.0 1.0 C6 A:CIT302 2.6 25.7 1.0 CG A:ASP172 2.7 19.8 1.0 OD2 A:ASP172 2.9 24.2 1.0 CE1 A:HIS249 2.9 24.6 1.0 CD2 A:HIS168 3.0 21.5 1.0 CE1 A:HIS168 3.1 21.4 1.0 CG A:HIS249 3.1 20.2 1.0 CB A:HIS249 3.5 18.7 1.0 C3 A:CIT302 4.0 27.2 1.0 NH2 A:ARG158 4.1 21.8 1.0 NE2 A:HIS249 4.1 20.6 1.0 ND1 A:HIS168 4.2 20.6 1.0 CB A:ASP172 4.2 20.5 1.0 CG A:HIS168 4.2 18.7 1.0 CD2 A:HIS249 4.2 19.7 1.0 CA A:HIS249 4.3 19.4 1.0 NH1 A:ARG158 4.3 22.5 1.0 NE2 A:HIS247 4.4 28.0 1.0 C4 A:CIT302 4.4 29.1 1.0 N A:ASP172 4.5 17.5 1.0 O1 A:CIT302 4.6 36.3 1.0 CA A:ASP172 4.6 16.5 1.0 C A:THR171 4.6 18.9 1.0 CZ A:ARG158 4.6 23.8 1.0 O A:THR171 4.7 20.5 1.0 C A:GLY170 4.7 16.6 1.0 CD2 A:HIS247 4.8 28.6 1.0 O A:HOH515 4.8 30.6 1.0 O A:HOH556 4.8 47.4 1.0 N A:THR171 4.8 17.0 1.0 O7 A:CIT302 4.9 28.5 1.0 O A:GLY170 4.9 21.5 1.0 C2 A:CIT302 4.9 26.6 1.0

S.Mobashery, H.J.Yoon, S.W.Suh, H.H.Lee, S.Ryu, M.J.Lee, D.Hesek, K.J.Min, D.R.An, N.Rana, S.J.Park, B.M.Kim, J.S.Kim. Peptidoglycan Reshaping By A Noncanonical Peptidase For Helical Cell Shape in Campylobacter Jejuni Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-019-13934-4