Zinc in PDB 4f78: Crystal Structure of Vancomycin Resistance D,D-Dipeptidase Vanxyg

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase Vanxyg, PDB code: 4f78 was solved by P.J.Stogios, Z.Wawrzak, E.Evdokimova, G.Minasov, O.Egorova, R.Di Leo, M.Kudritska, V.Yim, D.Meziane-Cherif, P.Courvalin, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.58 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.912, 43.960, 80.199, 90.00, 99.19, 90.00
R / Rfree (%)	15.4 / 18.6

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase Vanxyg 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 Vanxyg (pdb code 4f78). 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, PDB code: 4f78:

Zinc binding site 1 out of 1 in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase Vanxyg


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.9 occ:1.00 OD1 A:ASP114 2.2 13.1 1.0 ND1 A:HIS167 2.2 13.3 1.0 O A:HOH418 2.2 19.6 1.0 NE2 A:HIS107 2.2 16.9 1.0 OD2 A:ASP114 2.6 12.6 1.0 CG A:ASP114 2.7 16.4 1.0 O2 A:SO4303 2.7 32.0 0.7 CE1 A:HIS167 2.9 11.6 1.0 CD2 A:HIS107 3.1 13.3 1.0 CE1 A:HIS107 3.3 15.4 1.0 CG A:HIS167 3.3 9.9 1.0 O4 A:SO4303 3.5 34.6 0.7 S A:SO4303 3.7 26.6 0.7 CB A:HIS167 3.8 9.6 1.0 NE2 A:HIS167 4.1 10.9 1.0 CB A:ASP114 4.2 13.1 1.0 OE1 A:GLU164 4.2 13.2 1.0 CG A:HIS107 4.3 15.8 1.0 CD2 A:HIS167 4.3 13.9 1.0 ND1 A:HIS107 4.3 17.1 1.0 O A:HOH499 4.4 37.6 1.0 NE1 A:TRP166 4.4 14.2 1.0 O3 A:SO4303 4.5 38.2 0.7 NH2 A:ARG74 4.5 27.7 1.0 O A:HOH460 4.6 36.3 1.0 O A:HOH483 4.6 34.1 1.0 CD1 A:TRP166 4.6 12.2 1.0 CA A:HIS167 4.7 10.5 1.0 CA A:ASP114 4.8 13.1 1.0 N A:ASP114 4.9 10.0 1.0 O1 A:SO4303 4.9 26.4 0.7 NH1 A:ARG74 5.0 19.1 1.0 CZ A:ARG74 5.0 24.1 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