Chlorine in PDB 4mur: Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant, PDB code: 4mur 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)	34.45 / 1.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.239, 44.725, 62.519, 86.27, 77.70, 63.74
R / Rfree (%)	15.5 / 19.9

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant (pdb code 4mur). 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, PDB code: 4mur:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:41.9 occ:1.00 O A:HOH598 2.2 47.7 1.0 NE2 A:GLN67 3.1 15.0 1.0 N A:ALA88 3.2 17.4 1.0 OG A:SER93 3.5 18.6 1.0 CB A:ALA88 3.6 23.0 1.0 O A:HOH522 3.6 37.9 1.0 O A:HOH438 3.8 41.4 1.0 NH1 A:ARG62 3.9 16.1 1.0 CA A:ALA88 4.0 17.1 1.0 O A:HOH595 4.0 25.1 1.0 CD A:GLN67 4.0 15.3 1.0 CB A:SER93 4.1 18.8 1.0 O A:HOH465 4.1 42.3 1.0 OE1 A:GLN67 4.1 15.2 1.0 C A:VAL87 4.2 20.4 1.0 CD2 A:HIS95 4.2 17.2 1.0 CA A:VAL87 4.2 14.1 1.0 CG1 A:VAL87 4.2 17.9 1.0 O A:ALA88 4.5 15.2 1.0 O A:PHE86 4.7 23.3 1.0 O A:HOH383 4.7 28.8 1.0 C A:ALA88 4.7 17.8 1.0 CB A:VAL87 4.8 14.7 1.0 NE2 A:HIS95 4.9 17.9 1.0 ZN A:ZN201 5.0 18.1 0.2 CA A:SER93 5.0 19.6 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:28.9 occ:0.75 O A:HOH528 2.9 48.7 1.0 NH2 A:ARG69 3.1 58.5 1.0 N B:LEU22 3.3 18.6 1.0 O B:HOH454 3.3 45.2 1.0 NE A:ARG69 3.4 44.7 1.0 CZ A:ARG69 3.5 55.1 1.0 CB B:LEU22 3.8 20.0 1.0 CD A:LYS65 3.8 63.4 1.0 CE A:LYS65 3.9 71.3 1.0 CA B:LEU22 4.0 15.2 1.0 CA B:HIS21 4.0 26.0 1.0 C B:HIS21 4.0 22.1 1.0 O B:LEU22 4.1 19.3 1.0 O B:PRO20 4.1 29.1 1.0 CG B:LEU22 4.2 19.0 1.0 CG A:LYS65 4.3 49.9 1.0 CG A:ARG69 4.3 20.2 1.0 O B:HOH506 4.3 26.3 0.5 CD1 B:LEU22 4.4 19.2 1.0 CD A:ARG69 4.4 27.6 1.0 C B:LEU22 4.5 16.9 1.0 NH1 A:ARG69 4.6 54.1 1.0 CB A:LYS65 4.6 31.9 1.0 CB B:HIS21 4.9 38.2 1.0 C B:PRO20 5.0 28.2 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:31.7 occ:0.85 O A:HOH470 2.8 52.9 1.0 O A:HOH455 3.2 45.0 1.0 ND2 A:ASN8 3.2 17.6 1.0 CE1 A:HIS11 3.5 31.5 1.0 ND1 A:HIS11 3.7 30.5 1.0 ND2 A:ASN10 3.7 50.5 1.0 OD1 A:ASN8 4.0 21.7 1.0 CG A:ASN8 4.0 20.9 1.0 CB A:ASN10 4.0 28.6 1.0 O A:HOH508 4.1 58.8 1.0 O A:HOH425 4.1 36.9 1.0 CG A:GLU176 4.1 15.0 1.0 CG A:ASN10 4.4 42.6 1.0 CD2 A:LEU6 4.6 24.7 1.0 O A:HOH367 4.7 31.3 1.0 NE2 A:HIS11 4.8 31.2 1.0 O A:ILE147 4.9 20.9 1.0 OE2 A:GLU176 5.0 18.0 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:33.7 occ:0.80 O B:HOH583 2.3 32.2 1.0 NE2 B:GLN67 3.1 11.7 1.0 N B:ALA88 3.2 12.5 1.0 O B:HOH361 3.2 37.6 1.0 O B:HOH421 3.4 36.8 1.0 CB B:ALA88 3.7 14.8 1.0 OG B:SER93 3.8 16.7 1.0 O B:HOH353 3.9 32.0 1.0 NH1 B:ARG62 3.9 15.8 1.0 CA B:VAL87 3.9 12.0 1.0 CA B:ALA88 4.0 12.3 1.0 C B:VAL87 4.0 15.7 1.0 CD B:GLN67 4.0 12.6 1.0 O B:PHE86 4.2 22.7 1.0 OE1 B:GLN67 4.2 12.3 1.0 CD2 B:HIS95 4.3 15.3 1.0 CG1 B:VAL87 4.4 15.3 1.0 O B:HOH577 4.4 28.1 1.0 CB B:SER93 4.5 16.7 1.0 O B:HOH385 4.5 29.4 1.0 O B:ALA88 4.6 13.7 1.0 CB B:VAL87 4.8 11.6 1.0 CD2 B:LEU70 4.8 12.8 1.0 C B:ALA88 4.8 11.5 1.0 ZN B:ZN201 4.9 19.5 0.2 O B:HOH354 4.9 32.7 1.0 N B:VAL87 5.0 14.4 1.0 NE2 B:HIS95 5.0 18.1 1.0 C B:PHE86 5.0 19.5 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl204 b:32.1 occ:1.00 NH2 B:ARG69 2.9 21.7 1.0 O A:HOH580 3.1 40.9 1.0 N A:LEU22 3.2 16.9 1.0 NE B:ARG69 3.4 16.6 1.0 ND1 A:HIS21 3.5 44.6 1.0 O A:LEU22 3.5 14.1 1.0 CA A:HIS21 3.6 21.1 1.0 CZ B:ARG69 3.6 20.7 1.0 CB A:HIS21 3.8 22.2 1.0 C A:HIS21 3.9 19.9 1.0 O A:HOH520 4.0 27.4 1.0 CG A:HIS21 4.1 37.4 1.0 O B:HOH339 4.2 21.8 1.0 O B:HOH325 4.2 18.6 0.5 CA A:LEU22 4.3 13.8 1.0 C A:LEU22 4.3 12.6 1.0 O B:HOH480 4.6 40.4 1.0 CE1 A:HIS21 4.6 51.5 1.0 CD B:ARG69 4.7 15.4 1.0 CE B:LYS65 4.8 32.1 1.0 N A:HIS21 4.9 27.1 1.0 NH1 B:ARG69 4.9 13.5 1.0 CB A:LEU22 4.9 18.0 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl205 b:17.4 occ:0.50 O A:HOH538 2.9 49.1 1.0 O B:HOH436 3.0 33.9 1.0 OG1 B:THR63 3.0 15.2 1.0 O B:HOH492 3.7 37.6 1.0 CG2 B:THR63 3.8 25.3 1.0 CB B:THR63 3.8 18.6 1.0 CB B:LYS65 3.8 15.0 1.0 CE2 A:TYR61 3.8 23.4 1.0 CD B:LYS65 3.8 23.6 1.0 OH A:TYR61 4.1 34.9 1.0 CG B:LYS65 4.2 13.7 1.0 CG2 A:THR63 4.3 25.1 1.0 CG B:GLU66 4.3 11.5 1.0 CZ A:TYR61 4.4 26.6 1.0 CD B:GLU66 4.5 21.2 1.0 CD1 A:LEU22 4.6 23.8 1.0 OE2 B:GLU66 4.6 23.2 1.0 O B:HOH461 4.7 56.4 1.0 O B:HOH315 4.7 20.6 1.0 N B:GLU66 4.7 8.5 1.0 CD2 A:TYR61 4.8 23.1 1.0 O B:HOH567 4.9 59.2 1.0 CA B:LYS65 5.0 9.7 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