Copper in PDB 4oak: Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine-D-Alanine and Copper (II)

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine-D-Alanine and Copper (II), PDB code: 4oak 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)	19.33 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.939, 43.083, 66.316, 80.53, 74.52, 64.01
R / Rfree (%)	18.9 / 23.5

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine-D-Alanine and Copper (II) also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	6 atoms

The binding sites of Copper atom in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine-D-Alanine and Copper (II) (pdb code 4oak). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine-D-Alanine and Copper (II), PDB code: 4oak:
Jump to Copper binding site number: 1; 2;

Copper 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-Alanine-D-Alanine and Copper (II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine-D-Alanine and Copper (II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:20.3 occ:0.73 ND1 A:HIS156 2.0 18.2 1.0 O A:DAL202 2.0 33.5 0.9 OD1 A:ASP102 2.0 27.8 1.0 NE2 A:HIS95 2.2 18.5 1.0 N A:DAL202 2.5 31.4 0.9 CG A:ASP102 2.7 27.6 1.0 CE1 A:HIS156 2.7 20.8 1.0 OD2 A:ASP102 2.8 26.6 1.0 C A:DAL202 2.9 30.0 0.9 CE1 A:HIS95 3.0 16.5 1.0 CG A:HIS156 3.2 15.4 1.0 CA A:DAL202 3.2 30.6 0.9 CD2 A:HIS95 3.3 16.7 1.0 CB A:HIS156 3.7 17.1 1.0 NE2 A:HIS156 3.9 16.2 1.0 N A:DAL203 4.0 25.3 0.9 NH2 A:ARG62 4.0 15.8 0.5 CB A:ASP102 4.1 24.2 1.0 CB A:DAL202 4.1 29.8 0.9 CD2 A:HIS156 4.1 14.9 1.0 ND1 A:HIS95 4.2 16.7 1.0 CG A:HIS95 4.4 16.9 1.0 O A:ILE101 4.4 17.9 1.0 CA A:HIS156 4.5 14.9 1.0 CA A:DAL203 4.5 23.6 0.9 CA A:ASP102 4.5 20.7 1.0 OE1 A:GLU153 4.6 30.3 1.0 C A:ILE101 4.7 19.4 1.0 N A:ASP102 4.7 21.1 1.0 NE1 A:TRP155 4.9 44.8 1.0 C A:DAL203 4.9 26.0 0.9 CZ A:ARG62 5.0 17.4 0.5

Copper 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-Alanine-D-Alanine and Copper (II)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine-D-Alanine and Copper (II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:28.1 occ:0.88 O B:DAL202 1.9 45.4 1.0 NE2 B:HIS95 1.9 19.1 1.0 OD1 B:ASP102 1.9 27.1 1.0 ND1 B:HIS156 2.1 21.3 1.0 OD2 B:ASP102 2.1 22.1 1.0 CG B:ASP102 2.2 23.7 1.0 CE1 B:HIS156 2.7 20.9 1.0 CE1 B:HIS95 2.7 15.4 1.0 CD2 B:HIS95 3.1 18.4 1.0 C B:DAL202 3.1 47.4 1.0 CG B:HIS156 3.3 17.6 1.0 N B:DAL202 3.5 51.8 1.0 CB B:ASP102 3.7 23.0 1.0 NE2 B:HIS156 3.9 18.8 1.0 CA B:DAL202 3.9 50.6 1.0 ND1 B:HIS95 3.9 19.8 1.0 CB B:HIS156 4.0 21.2 1.0 N B:DAL203 4.1 42.9 1.0 CG B:HIS95 4.1 19.6 1.0 CD2 B:HIS156 4.2 16.4 1.0 CA B:ASP102 4.3 21.3 1.0 CA B:DAL203 4.3 40.4 1.0 O B:ILE101 4.3 18.6 1.0 N B:ASP102 4.3 20.2 1.0 C B:ILE101 4.4 19.9 1.0 NH1 B:ARG62 4.5 28.0 1.0 NH2 B:ARG62 4.6 26.3 1.0 CA B:HIS156 4.6 19.3 1.0 C B:DAL203 4.7 39.9 1.0 NE1 B:TRP155 4.9 39.0 1.0 CD1 B:TRP155 4.9 37.0 1.0 CB B:DAL202 5.0 51.4 1.0 OE1 B:GLU153 5.0 31.7 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