Zinc in PDB 4muq: Crystal Structure of Vancomycin Resistance D,D-Dipeptidase Vanxyg in Complex with D-Ala-D-Ala Phosphinate Analog

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase Vanxyg in Complex with D-Ala-D-Ala Phosphinate Analog, PDB code: 4muq 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)	38.40 / 1.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.895, 43.728, 80.236, 90.00, 99.20, 90.00
R / Rfree (%)	16.2 / 18.5

The binding sites of Zinc atom in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase Vanxyg in Complex with D-Ala-D-Ala Phosphinate Analog (pdb code 4muq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase Vanxyg in Complex with D-Ala-D-Ala Phosphinate Analog, PDB code: 4muq:

Zinc binding site 1 out of 1 in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase Vanxyg 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 Vanxyg in Complex with D-Ala-D-Ala Phosphinate Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.3 occ:0.66 OD1 A:ASP114 2.0 12.4 1.0 NE2 A:HIS107 2.0 9.6 1.0 ND1 A:HIS167 2.1 10.6 1.0 O32 A:LY0302 2.2 5.6 0.5 O32 A:2D8303 2.2 42.6 0.5 OD2 A:ASP114 2.4 19.4 1.0 O31 A:LY0302 2.4 9.9 0.5 O31 A:2D8303 2.4 51.8 0.5 CG A:ASP114 2.5 14.1 1.0 P A:LY0302 2.9 38.2 0.5 P A:2D8303 2.9 5.8 0.5 CE1 A:HIS167 2.9 12.1 1.0 CE1 A:HIS107 3.0 10.3 1.0 CD2 A:HIS107 3.0 11.4 1.0 CG A:HIS167 3.2 8.8 1.0 CB A:HIS167 3.6 10.0 1.0 CB A:ASP114 4.0 11.8 1.0 NE2 A:HIS167 4.1 9.7 1.0 ND1 A:HIS107 4.1 9.8 1.0 C4 A:2D8303 4.1 14.5 0.5 C4 A:LY0302 4.1 14.7 0.5 CG A:HIS107 4.2 9.8 1.0 N1 A:2D8303 4.2 16.8 0.5 C5 A:LY0302 4.2 9.3 0.5 C5 A:2D8303 4.2 11.4 0.5 C2 A:LY0302 4.2 37.5 0.5 CD2 A:HIS167 4.2 9.7 1.0 C2 A:2D8303 4.2 9.9 0.5 NE1 A:TRP166 4.3 14.6 1.0 NH1 A:ARG74 4.4 14.7 1.0 OE1 A:GLU164 4.5 15.6 1.0 CD1 A:TRP166 4.5 13.5 1.0 CA A:HIS167 4.5 9.4 1.0 CA A:ASP114 4.6 9.8 1.0 N A:ASP114 4.6 9.5 1.0 C6 A:LY0302 4.7 8.7 0.5 C6 A:2D8303 4.7 17.7 0.5 O61 A:LY0302 4.7 28.1 0.5 O61 A:2D8303 4.7 5.0 0.5 NH2 A:ARG74 4.8 13.3 1.0 C A:ILE113 4.9 9.6 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