Zinc in PDB 6ue4: Shya Endopeptidase From Vibrio Cholerae (Closed Form)

The structure of Shya Endopeptidase From Vibrio Cholerae (Closed Form), PDB code: 6ue4 was solved by Y.Mao, A.Sulpizio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.55 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.115, 87.252, 74.973, 90.00, 100.37, 90.00
R / Rfree (%)	17.8 / 23.3

The binding sites of Zinc atom in the Shya Endopeptidase From Vibrio Cholerae (Closed Form) (pdb code 6ue4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Shya Endopeptidase From Vibrio Cholerae (Closed Form), PDB code: 6ue4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Shya Endopeptidase From Vibrio Cholerae (Closed Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Shya Endopeptidase From Vibrio Cholerae (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:24.4 occ:1.00 ND1 A:HIS378 1.9 16.8 1.0 NE2 A:HIS297 2.0 23.5 1.0 OD1 A:ASP301 2.0 22.7 1.0 O A:HOH632 2.2 18.1 1.0 CG A:ASP301 2.7 21.3 1.0 OD2 A:ASP301 2.7 20.8 1.0 CE1 A:HIS378 2.9 16.0 1.0 CE1 A:HIS297 2.9 23.5 1.0 CG A:HIS378 3.0 16.4 1.0 CD2 A:HIS297 3.0 23.7 1.0 CB A:HIS378 3.4 17.0 1.0 O A:HOH636 3.9 32.1 1.0 ND1 A:HIS297 4.0 23.0 1.0 NE2 A:HIS376 4.0 20.3 1.0 NE2 A:HIS378 4.0 14.9 1.0 CD2 A:HIS378 4.1 16.6 1.0 CG A:HIS297 4.1 23.6 1.0 CB A:ASP301 4.2 20.3 1.0 CA A:HIS378 4.3 16.8 1.0 NH1 A:ARG286 4.4 50.8 1.0 CD2 A:HIS376 4.4 20.5 1.0 CA A:ASP301 4.7 20.1 1.0 N A:ASP301 4.7 18.3 1.0 O A:GLY299 4.7 16.7 1.0 C A:THR300 4.8 18.4 1.0 C A:GLY299 4.9 17.3 1.0 O A:THR300 4.9 18.5 1.0

Zinc binding site 2 out of 2 in the Shya Endopeptidase From Vibrio Cholerae (Closed Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Shya Endopeptidase From Vibrio Cholerae (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:24.6 occ:1.00 ND1 B:HIS378 2.0 15.9 1.0 OD1 B:ASP301 2.0 18.0 1.0 NE2 B:HIS297 2.1 22.4 1.0 O B:HOH655 2.1 24.0 1.0 CG B:ASP301 2.7 19.4 1.0 OD2 B:ASP301 2.8 19.6 1.0 CE1 B:HIS378 2.8 16.7 1.0 CD2 B:HIS297 3.0 21.8 1.0 CG B:HIS378 3.0 16.4 1.0 CE1 B:HIS297 3.1 23.4 1.0 CB B:HIS378 3.5 16.9 1.0 NE2 B:HIS376 4.0 22.6 1.0 NH1 B:ARG286 4.0 53.2 1.0 NE2 B:HIS378 4.0 16.2 1.0 O B:HOH625 4.1 31.6 1.0 CD2 B:HIS378 4.1 16.5 1.0 CB B:ASP301 4.2 19.0 1.0 CG B:HIS297 4.2 21.1 1.0 ND1 B:HIS297 4.2 21.8 1.0 CA B:HIS378 4.4 17.5 1.0 CD2 B:HIS376 4.4 22.3 1.0 N B:ASP301 4.7 19.2 1.0 CA B:ASP301 4.7 19.6 1.0 O B:GLY299 4.8 19.3 1.0 C B:THR300 4.8 18.6 1.0 C B:GLY299 4.9 19.0 1.0

J.H.Shin, A.G.Sulpizio, A.Kelley, L.Alvarez, S.G.Murphy, L.Fan, F.Cava, Y.Mao, M.A.Saper, T.Dorr. Structural Basis of Peptidoglycan Endopeptidase Regulation. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 32393643
DOI: 10.1073/PNAS.2001661117