Zinc in PDB 4mur: Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant, PDB code: 4mur was solved by P.J.Stogios, E.Evdokimova, D.Meziane-Cherif, R.Di Leo, V.Yim, P.Courvalin, A.Savchenko, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.45 / 1.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.239, 44.725, 62.519, 86.27, 77.70, 63.74
R / Rfree (%)	15.5 / 19.9

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant (pdb code 4mur). 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 Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant, PDB code: 4mur:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant


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 Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:18.1 occ:0.17 OD1 A:ASP102 2.0 21.2 1.0 O A:HOH383 2.1 28.8 1.0 NE2 A:HIS95 2.1 17.9 1.0 ND1 A:HIS156 2.2 26.5 1.0 OD2 A:ASP102 2.2 30.7 1.0 CG A:ASP102 2.4 19.0 1.0 O A:HOH465 2.6 42.3 1.0 CE1 A:HIS156 2.8 21.0 1.0 CE1 A:HIS95 3.0 18.9 1.0 CD2 A:HIS95 3.1 17.2 1.0 CG A:HIS156 3.4 10.8 1.0 O A:HOH598 3.9 47.7 1.0 CB A:ASP102 3.9 9.1 1.0 NE2 A:HIS156 4.0 14.4 1.0 CB A:HIS156 4.0 5.8 1.0 ND1 A:HIS95 4.2 16.4 1.0 CG A:HIS95 4.3 14.1 1.0 CD2 A:HIS156 4.3 14.9 1.0 NE1 A:TRP155 4.4 12.7 1.0 CA A:ASP102 4.6 11.1 1.0 OE1 A:GLU153 4.6 15.7 1.0 CD1 A:TRP155 4.6 13.3 1.0 N A:ASP102 4.7 10.0 1.0 O A:ILE101 4.7 13.3 1.0 CA A:HIS156 4.8 6.2 1.0 C A:ILE101 4.9 13.8 1.0 O A:HOH414 4.9 36.2 1.0 O A:HOH438 4.9 41.4 1.0 CL A:CL202 5.0 41.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant


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 Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:19.5 occ:0.25 OD1 B:ASP102 2.0 20.0 1.0 ND1 B:HIS156 2.0 17.3 1.0 O B:HOH385 2.1 29.4 1.0 NE2 B:HIS95 2.1 18.1 1.0 CE1 B:HIS156 2.7 20.8 1.0 CG B:ASP102 2.9 23.4 1.0 OD2 B:ASP102 3.0 26.8 1.0 O B:HOH353 3.0 32.0 1.0 CD2 B:HIS95 3.0 15.3 1.0 CE1 B:HIS95 3.1 16.3 1.0 CG B:HIS156 3.2 10.3 1.0 CB B:HIS156 3.8 10.2 1.0 NE2 B:HIS156 3.8 14.7 1.0 O B:HOH583 4.0 32.2 1.0 CD2 B:HIS156 4.1 13.8 1.0 ND1 B:HIS95 4.2 17.8 1.0 CG B:HIS95 4.2 15.6 1.0 CB B:ASP102 4.3 12.9 1.0 OE1 B:GLU153 4.4 21.4 1.0 O B:HOH354 4.4 32.7 1.0 NE1 B:TRP155 4.5 20.0 1.0 CA B:HIS156 4.7 10.1 1.0 CD1 B:TRP155 4.7 16.5 1.0 O B:HOH421 4.7 36.8 1.0 O B:ILE101 4.8 15.9 1.0 CA B:ASP102 4.8 9.9 1.0 CL B:CL203 4.9 33.7 0.8 N B:ASP102 4.9 11.7 1.0 C B:ILE101 5.0 17.0 1.0

D.Meziane-Cherif, P.J.Stogios, E.Evdokimova, A.Savchenko, P.Courvalin. Structural Basis For the Evolution of Vancomycin Resistance D,D-Peptidases. Proc.Natl.Acad.Sci.Usa V. 111 5872 2014.
ISSN: ISSN 0027-8424
PubMed: 24711382
DOI: 10.1073/PNAS.1402259111