Chlorine 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
Copper	(Cu)	2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 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 Chlorine with other atoms in the Cl 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:Cl206 b:51.9 occ:1.00 O A:HOH311 3.3 30.0 1.0 N A:LEU80 3.7 21.4 1.0 CA A:GLY79 3.9 24.6 1.0 O A:HOH399 4.1 43.3 1.0 C A:GLY79 4.3 21.9 1.0 CB A:LEU80 4.6 22.5 1.0 CA A:LEU80 4.8 20.5 1.0

Chlorine binding site 2 out of 6 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 Chlorine with other atoms in the Cl 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 A:Cl207 b:56.1 occ:1.00 O B:HOH393 2.6 68.3 1.0 NH2 A:ARG69 2.8 36.5 1.0 NE A:ARG69 3.3 30.6 1.0 O A:HOH462 3.4 42.1 1.0 CZ A:ARG69 3.5 35.1 1.0 O B:HOH382 3.6 34.5 1.0 O A:HOH372 3.7 38.0 1.0 N B:LEU22 4.2 22.1 1.0 O B:LEU22 4.2 21.3 1.0 CD A:ARG69 4.6 24.9 1.0 ND1 B:HIS21 4.6 46.4 1.0 CE A:LYS65 4.6 46.6 1.0 CA B:HIS21 4.7 29.5 1.0 NH1 A:ARG69 4.8 33.8 1.0 NZ A:LYS65 4.8 52.1 1.0 CG A:ARG69 4.9 22.0 1.0 CA B:LEU22 5.0 21.8 1.0 C B:HIS21 5.0 22.9 1.0

Chlorine binding site 3 out of 6 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl208 b:59.9 occ:1.00 O A:HOH342 3.3 35.9 1.0 OG1 A:THR63 3.5 24.8 1.0 O B:HOH315 3.5 47.6 1.0 O A:HOH352 3.7 28.6 1.0 CG2 A:THR63 4.0 28.6 1.0 CB A:THR63 4.2 26.0 1.0 NH1 A:ARG69 4.3 33.8 1.0 CG A:GLU66 4.5 21.3 1.0 CD A:LYS65 4.5 43.2 1.0 OE2 A:GLU66 4.6 27.9 1.0 CG2 B:THR63 4.6 26.7 1.0 CB A:LYS65 4.6 30.1 1.0 O2 B:SO4205 4.7 63.1 1.0 CD A:GLU66 4.7 24.4 1.0 CE2 B:TYR61 4.8 23.2 1.0 CG A:LYS65 4.9 36.8 1.0

Chlorine binding site 4 out of 6 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl209 b:53.4 occ:1.00 O A:HOH349 2.8 40.8 1.0 CE1 A:HIS11 3.3 39.3 1.0 O A:HOH446 3.4 52.1 1.0 O A:HOH324 3.7 41.2 1.0 ND1 A:HIS11 3.8 36.0 1.0 ND2 A:ASN8 3.8 19.9 1.0 CG A:GLU176 4.2 19.9 1.0 ND2 A:ASN10 4.3 42.2 1.0 NE2 A:HIS11 4.5 41.8 1.0 CB A:ASN10 4.6 36.4 1.0 CD2 A:LEU6 4.6 24.3 1.0 CG A:ASN8 4.6 21.5 1.0 OD1 A:ASN8 4.7 25.9 1.0 CB A:GLU176 4.8 19.3 1.0 O A:HOH447 4.8 54.8 1.0

Chlorine binding site 5 out of 6 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl206 b:50.5 occ:1.00 O B:HOH395 3.2 35.5 1.0 O B:HOH378 3.6 33.0 1.0 NE2 B:HIS11 3.7 36.6 1.0 CG B:GLU176 4.0 18.6 1.0 CD2 B:HIS11 4.0 33.5 1.0 ND2 B:ASN8 4.1 21.6 1.0 OD1 B:ASN10 4.1 56.4 1.0 CB B:GLU176 4.4 19.9 1.0 CD2 B:LEU6 4.4 20.3 1.0 O B:HOH424 4.5 28.6 0.5 O B:HOH418 4.5 32.4 1.0 CB B:ASN10 4.6 43.8 1.0 CG B:ASN10 4.8 52.5 1.0 CE1 B:HIS11 4.9 37.4 1.0

Chlorine binding site 6 out of 6 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl207 b:60.2 occ:1.00 N B:ASP143 3.3 43.0 1.0 CA B:ASP143 3.9 43.4 1.0 N B:TYR152 4.2 29.5 1.0 CB B:TYR152 4.3 30.4 1.0 CB B:GLN145 4.3 48.4 1.0 C B:GLU142 4.3 41.1 1.0 CA B:GLU142 4.4 39.5 1.0 N B:LYS144 4.6 31.8 1.0 CG B:GLU142 4.7 53.6 1.0 O B:HOH399 4.7 64.3 1.0 CA B:TYR152 4.8 26.7 1.0 N B:GLN145 4.8 36.0 1.0 C B:ASP143 4.8 38.4 1.0 CA B:SER151 5.0 30.0 1.0 OD1 B:ASP143 5.0 58.9 1.0 O B:PRO141 5.0 23.0 1.0 CG B:ASP143 5.0 54.7 1.0 C B:SER151 5.0 29.9 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