Zinc in PDB 5opz: Crystal Structure of Serratia Marcescens L-Ala D-Glu Endopeptidase Chix

The structure of Crystal Structure of Serratia Marcescens L-Ala D-Glu Endopeptidase Chix, PDB code: 5opz was solved by R.A.Owen, P.K.Fyfe, A.Lodge, J.Biboy, W.Vollmer, W.N.Hunter, F.Sargent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.78 / 1.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.627, 55.531, 51.780, 90.00, 90.00, 90.00
R / Rfree (%)	8.9 / 12

The structure of Crystal Structure of Serratia Marcescens L-Ala D-Glu Endopeptidase Chix also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Serratia Marcescens L-Ala D-Glu Endopeptidase Chix (pdb code 5opz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Serratia Marcescens L-Ala D-Glu Endopeptidase Chix, PDB code: 5opz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Serratia Marcescens L-Ala D-Glu Endopeptidase Chix


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Serratia Marcescens L-Ala D-Glu Endopeptidase Chix within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:7.5 occ:1.00 OE2 B:GLU8 2.0 7.6 1.0 OD1 A:ASP76 2.0 7.0 1.0 ND1 A:HIS124 2.1 5.5 1.0 NE2 A:HIS69 2.1 5.9 1.0 CD B:GLU8 2.7 7.8 1.0 OE1 B:GLU8 2.7 10.6 1.0 CG A:ASP76 2.8 6.7 1.0 CE1 A:HIS124 2.9 5.7 1.0 OD2 A:ASP76 2.9 10.4 1.0 CE1 A:HIS69 3.1 6.3 1.0 CD2 A:HIS69 3.1 5.0 1.0 CG A:HIS124 3.1 5.1 1.0 CB A:HIS124 3.6 4.4 1.0 NE2 A:HIS124 4.0 5.7 1.0 NH2 A:ARG48 4.1 8.0 1.0 CG B:GLU8 4.1 9.0 1.0 ND1 A:HIS69 4.2 6.8 1.0 CD2 A:HIS124 4.2 5.9 1.0 CA A:HIS124 4.2 4.5 1.0 CB A:ASP76 4.2 6.5 1.0 CG A:HIS69 4.2 5.9 1.0 O A:VAL75 4.4 6.1 1.0 CB B:GLU7 4.4 11.3 1.0 N A:ASP76 4.6 4.8 1.0 C A:VAL75 4.6 4.9 1.0 O A:HOH334 4.7 17.8 1.0 CA A:ASP76 4.7 5.6 1.0 O A:HOH432 4.8 14.8 1.0 OE1 B:GLU7 4.8 14.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Serratia Marcescens L-Ala D-Glu Endopeptidase Chix


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Serratia Marcescens L-Ala D-Glu Endopeptidase Chix within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:7.5 occ:1.00 OD1 B:ASP76 2.0 6.0 1.0 ND1 B:HIS124 2.0 4.5 1.0 NE2 B:HIS69 2.1 5.3 1.0 CG B:ASP76 2.8 6.2 1.0 CE1 B:HIS124 2.9 4.5 1.0 OD2 B:ASP76 2.9 9.8 1.0 CE1 B:HIS69 3.0 5.7 1.0 CD2 B:HIS69 3.1 5.3 1.0 CG B:HIS124 3.1 4.6 1.0 CB B:HIS124 3.6 4.3 1.0 NE2 B:HIS124 4.1 4.9 1.0 NH2 B:ARG48 4.1 7.3 1.0 CA B:HIS124 4.1 4.4 1.0 ND1 B:HIS69 4.2 5.0 1.0 CD2 B:HIS124 4.2 5.2 1.0 CG B:HIS69 4.2 5.6 1.0 CB B:ASP76 4.2 5.5 1.0 O B:VAL75 4.4 5.2 1.0 N B:ASP76 4.6 5.1 1.0 C B:VAL75 4.6 4.5 1.0 O B:HOH403 4.7 16.1 1.0 CA B:ASP76 4.7 5.5 1.0 O B:HOH306 4.8 18.8 1.0

R.A.Owen, P.K.Fyfe, A.Lodge, J.Biboy, W.Vollmer, W.N.Hunter, F.Sargent. Structure and Activity of Chix: A Peptidoglycan Hydrolase Required For Chitinase Secretion By Serratia Marcescens. Biochem. J. V. 475 415 2018.
ISSN: ESSN 1470-8728
PubMed: 29229757
DOI: 10.1042/BCJ20170633