Zinc in PDB 6jn7: Structure of H216A Mutant Closed Form Peptidoglycan Peptidase

The structure of Structure of H216A Mutant Closed Form Peptidoglycan Peptidase, PDB code: 6jn7 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)	32.70 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.304, 105.632, 86.161, 90.00, 107.22, 90.00
R / Rfree (%)	16.7 / 19.4

The binding sites of Zinc atom in the Structure of H216A Mutant Closed Form Peptidoglycan Peptidase (pdb code 6jn7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of H216A Mutant Closed Form Peptidoglycan Peptidase, PDB code: 6jn7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of H216A Mutant Closed Form 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 H216A Mutant Closed Form Peptidoglycan Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:26.3 occ:1.00 ND1 A:HIS249 2.0 18.2 1.0 O2 A:TAR302 2.1 28.8 1.0 O3 A:TAR302 2.1 41.6 1.0 OD1 A:ASP172 2.1 36.9 1.0 NE2 A:HIS168 2.1 20.4 1.0 C2 A:TAR302 2.4 47.2 1.0 C3 A:TAR302 2.7 51.7 1.0 CG A:ASP172 2.8 27.1 1.0 OD2 A:ASP172 2.9 24.5 1.0 CE1 A:HIS249 3.0 26.2 1.0 CG A:HIS249 3.1 21.9 1.0 CD2 A:HIS168 3.1 16.1 1.0 CE1 A:HIS168 3.1 20.6 1.0 CB A:HIS249 3.5 19.2 1.0 C4 A:TAR302 3.6 53.7 1.0 O4 A:TAR302 3.6 68.4 1.0 C1 A:TAR302 3.9 45.9 1.0 NH2 A:ARG158 4.1 21.5 1.0 NE2 A:HIS249 4.1 20.2 1.0 CD2 A:HIS249 4.2 18.1 1.0 ND1 A:HIS168 4.2 20.5 1.0 CG A:HIS168 4.2 18.5 1.0 CB A:ASP172 4.3 19.6 1.0 CA A:HIS249 4.3 22.5 1.0 NE2 A:HIS247 4.3 30.2 1.0 O11 A:TAR302 4.5 59.2 1.0 NH1 A:ARG158 4.5 23.3 1.0 O41 A:TAR302 4.6 46.8 1.0 O1 A:TAR302 4.7 67.1 1.0 CD2 A:HIS247 4.7 27.8 1.0 N A:ASP172 4.7 17.0 1.0 CZ A:ARG158 4.8 24.0 1.0 CA A:ASP172 4.8 17.6 1.0 C A:THR171 4.9 19.1 1.0 C A:GLY170 4.9 22.0 1.0

Zinc binding site 2 out of 3 in the Structure of H216A Mutant Closed Form Peptidoglycan Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of H216A Mutant Closed Form Peptidoglycan Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:25.1 occ:1.00 O3 B:TAR302 1.9 27.3 1.0 O2 B:TAR302 1.9 47.3 1.0 OD1 B:ASP172 2.1 20.8 1.0 ND1 B:HIS249 2.1 22.3 1.0 NE2 B:HIS168 2.2 18.2 1.0 C3 B:TAR302 2.4 43.8 1.0 C2 B:TAR302 2.7 36.6 1.0 CG B:ASP172 2.8 26.3 1.0 OD2 B:ASP172 2.9 24.1 1.0 CE1 B:HIS249 3.0 24.3 1.0 CE1 B:HIS168 3.1 21.3 1.0 CG B:HIS249 3.1 25.9 1.0 CD2 B:HIS168 3.1 16.1 1.0 CB B:HIS249 3.5 17.4 1.0 C1 B:TAR302 3.7 48.5 1.0 O11 B:TAR302 3.8 68.3 1.0 C4 B:TAR302 3.9 52.7 1.0 NH2 B:ARG158 4.1 22.1 1.0 NE2 B:HIS249 4.2 22.0 1.0 NE2 B:HIS247 4.2 27.3 1.0 ND1 B:HIS168 4.2 20.1 1.0 CD2 B:HIS249 4.2 24.1 1.0 CB B:ASP172 4.2 19.4 1.0 CG B:HIS168 4.3 19.1 1.0 CA B:HIS249 4.3 21.7 1.0 O4 B:TAR302 4.4 41.0 1.0 NH1 B:ARG158 4.5 21.0 1.0 CD2 B:HIS247 4.5 26.3 1.0 N B:ASP172 4.7 19.2 1.0 CG1 B:VAL243 4.7 40.1 1.0 CA B:ASP172 4.7 18.2 1.0 CZ B:ARG158 4.8 23.4 1.0 O41 B:TAR302 4.8 70.3 1.0 O1 B:TAR302 4.8 59.0 1.0 C B:THR171 4.9 23.3 1.0 C B:GLY170 4.9 27.6 1.0

Zinc binding site 3 out of 3 in the Structure of H216A Mutant Closed Form Peptidoglycan Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of H216A Mutant Closed Form Peptidoglycan Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:27.0 occ:1.00 O3 C:TAR302 1.8 36.0 1.0 ND1 C:HIS249 2.0 20.7 1.0 OD1 C:ASP172 2.1 21.1 1.0 NE2 C:HIS168 2.2 22.3 1.0 O11 C:TAR302 2.3 32.8 1.0 C3 C:TAR302 2.7 44.5 1.0 CG C:ASP172 2.8 20.8 1.0 OD2 C:ASP172 2.8 25.1 1.0 CE1 C:HIS249 2.9 21.7 1.0 C1 C:TAR302 2.9 45.6 1.0 C2 C:TAR302 2.9 49.4 1.0 CD2 C:HIS168 3.1 20.8 1.0 CG C:HIS249 3.1 23.6 1.0 CE1 C:HIS168 3.2 22.3 1.0 CB C:HIS249 3.5 25.2 1.0 C4 C:TAR302 4.0 59.5 1.0 NE2 C:HIS249 4.0 22.6 1.0 O1 C:TAR302 4.1 44.1 1.0 NH2 C:ARG158 4.1 20.4 1.0 CD2 C:HIS249 4.1 16.7 1.0 CG C:HIS168 4.2 21.8 1.0 ND1 C:HIS168 4.2 23.0 1.0 CB C:ASP172 4.2 18.4 1.0 CA C:HIS249 4.3 24.8 1.0 NE2 C:HIS247 4.3 27.7 1.0 O2 C:TAR302 4.4 64.6 1.0 NH1 C:ARG158 4.5 23.3 1.0 O41 C:TAR302 4.5 76.4 1.0 N C:ASP172 4.7 19.2 1.0 CD2 C:HIS247 4.7 30.3 1.0 CA C:ASP172 4.7 20.9 1.0 CZ C:ARG158 4.7 27.2 1.0 C C:THR171 4.8 19.3 1.0 O4 C:TAR302 4.9 76.6 1.0 C C:GLY170 4.9 24.3 1.0 N C:THR171 5.0 23.5 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