Zinc in PDB 4mus: Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Ala-D-Ala Phosphinate Analog

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Ala-D-Ala Phosphinate Analog, PDB code: 4mus 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)	37.20 / 1.68
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.256, 44.780, 62.407, 86.84, 77.29, 64.15
R / Rfree (%)	16.8 / 20.7

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Ala-D-Ala Phosphinate Analog also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Ala-D-Ala Phosphinate Analog (pdb code 4mus). 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 in Complex with D-Ala-D-Ala Phosphinate Analog, PDB code: 4mus:
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 in Complex with D-Ala-D-Ala Phosphinate Analog


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 in Complex with D-Ala-D-Ala Phosphinate Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:14.1 occ:0.60 OD1 A:ASP102 1.9 16.7 1.0 O32 A:LY0203 2.0 21.6 0.4 ND1 A:HIS156 2.0 15.5 1.0 NE2 A:HIS95 2.0 12.6 1.0 O32 A:2D8202 2.1 22.7 0.4 CG A:ASP102 2.7 18.1 1.0 O31 A:LY0203 2.8 24.5 0.4 O31 A:2D8202 2.8 28.3 0.4 CE1 A:HIS156 2.8 20.9 1.0 OD2 A:ASP102 2.9 20.2 1.0 P A:LY0203 2.9 22.3 0.4 P A:2D8202 3.0 19.2 0.4 CD2 A:HIS95 3.0 15.8 1.0 CE1 A:HIS95 3.0 14.6 1.0 CG A:HIS156 3.2 13.8 1.0 CB A:HIS156 3.7 12.6 1.0 NE2 A:HIS156 4.0 15.4 1.0 C5 A:LY0203 4.1 17.6 0.4 C5 A:2D8202 4.1 17.2 0.4 ND1 A:HIS95 4.1 17.9 1.0 C4 A:LY0203 4.1 13.5 0.4 CG A:HIS95 4.2 15.5 1.0 CB A:ASP102 4.2 15.9 1.0 C4 A:2D8202 4.2 14.6 0.4 CD2 A:HIS156 4.2 14.8 1.0 N1 A:2D8202 4.3 16.9 0.4 NH2 A:ARG62 4.3 20.6 1.0 C2 A:LY0203 4.3 16.5 0.4 NE1 A:TRP155 4.4 20.9 1.0 C2 A:2D8202 4.4 19.5 0.4 CA A:HIS156 4.4 13.1 1.0 CD1 A:TRP155 4.5 18.1 1.0 O61 A:LY0203 4.6 21.1 0.4 C6 A:LY0203 4.6 17.7 0.4 C6 A:2D8202 4.6 18.9 0.4 O61 A:2D8202 4.6 19.3 0.4 CA A:ASP102 4.6 15.7 1.0 O A:ILE101 4.6 16.5 1.0 N A:ASP102 4.7 15.1 1.0 OE1 A:GLU153 4.7 24.2 1.0 C A:ILE101 4.8 15.0 1.0 CB A:ALA100 4.9 16.8 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 in Complex with D-Ala-D-Ala Phosphinate Analog


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 in Complex with D-Ala-D-Ala Phosphinate Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:18.4 occ:0.31 OD1 B:ASP102 1.9 23.5 1.0 O31 B:LY0202 2.0 20.8 0.2 O31 B:2D8203 2.0 22.9 0.6 NE2 B:HIS95 2.1 16.7 1.0 ND1 B:HIS156 2.1 20.6 1.0 O32 B:LY0202 2.6 40.6 0.2 O32 B:2D8203 2.6 39.3 0.6 CG B:ASP102 2.6 20.2 1.0 OD2 B:ASP102 2.8 28.3 1.0 P B:LY0202 2.8 32.7 0.2 CE1 B:HIS156 2.8 22.2 1.0 P B:2D8203 2.8 44.3 0.6 CE1 B:HIS95 3.0 19.3 1.0 CD2 B:HIS95 3.1 18.4 1.0 CG B:HIS156 3.3 12.9 1.0 CB B:HIS156 3.8 10.7 1.0 C5 B:LY0202 3.9 26.2 0.2 NE2 B:HIS156 3.9 16.5 1.0 C4 B:LY0202 4.0 27.1 0.2 C5 B:2D8203 4.0 27.8 0.6 C4 B:2D8203 4.0 26.7 0.6 CB B:ASP102 4.1 14.0 1.0 ND1 B:HIS95 4.1 20.1 1.0 CD2 B:HIS156 4.2 15.1 1.0 CG B:HIS95 4.2 17.1 1.0 C2 B:LY0202 4.2 28.8 0.2 C2 B:2D8203 4.3 34.9 0.6 N1 B:2D8203 4.3 27.3 0.6 NE1 B:TRP155 4.3 16.4 1.0 C6 B:2D8203 4.4 22.6 0.6 C6 B:LY0202 4.4 23.4 0.2 O62 B:2D8203 4.4 26.7 0.6 O62 B:LY0202 4.4 26.0 0.2 CD1 B:TRP155 4.5 15.8 1.0 CA B:HIS156 4.6 9.4 1.0 CA B:ASP102 4.6 12.0 1.0 NH2 B:ARG62 4.6 32.0 1.0 OE1 B:GLU153 4.6 19.2 1.0 N B:ASP102 4.6 13.5 1.0 O B:ILE101 4.7 14.6 1.0 C B:ILE101 4.8 14.7 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