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Zinc in PDB 4mut: Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine

Protein crystallography data

The structure of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine, PDB code: 4mut 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) 34.57 / 2.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.674, 45.214, 63.014, 86.69, 77.20, 63.88
R / Rfree (%) 16.1 / 18.5

Other elements in 4mut:

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

Chlorine (Cl) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 4mut

Go back to Zinc Binding Sites List in 4mut
Zinc 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


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/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:29.6
occ:0.40
O A:HOH469 2.1 38.1 1.0
OD1 A:ASP102 2.1 23.8 1.0
O A:HOH468 2.1 54.6 1.0
ND1 A:HIS156 2.2 29.3 1.0
NE2 A:HIS95 2.2 35.1 1.0
CE1 A:HIS156 2.8 29.6 1.0
N A:DAL202 2.8 59.3 1.0
CG A:ASP102 3.0 33.9 1.0
OD2 A:ASP102 3.1 38.6 1.0
CE1 A:HIS95 3.2 28.9 1.0
CD2 A:HIS95 3.3 36.1 1.0
CG A:HIS156 3.4 27.0 1.0
CA A:DAL202 3.5 56.3 1.0
CB A:HIS156 4.0 28.8 1.0
NE2 A:HIS156 4.0 23.6 1.0
C A:DAL202 4.1 46.2 1.0
ND1 A:HIS95 4.3 34.4 1.0
O A:HOH407 4.3 51.3 1.0
CD2 A:HIS156 4.3 26.9 1.0
CG A:HIS95 4.4 34.8 1.0
O A:DAL202 4.4 48.8 1.0
NE1 A:TRP155 4.4 27.0 1.0
CB A:ASP102 4.4 24.9 1.0
OE1 A:GLU153 4.4 37.9 1.0
O A:HOH408 4.6 39.4 1.0
CD1 A:TRP155 4.7 28.0 1.0
OXT A:DAL202 4.7 49.2 1.0
CA A:HIS156 4.8 23.9 1.0
CA A:ASP102 4.9 24.3 1.0
CB A:DAL202 4.9 44.9 1.0
O A:ILE101 5.0 30.4 1.0
N A:ASP102 5.0 28.3 1.0

Zinc binding site 2 out of 2 in 4mut

Go back to Zinc Binding Sites List in 4mut
Zinc 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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Vancomycin Resistance D,D-Dipeptidase/D,D- Pentapeptidase Vanxyc D59S Mutant in Complex with D-Alanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:39.0
occ:0.70
O B:HOH444 2.1 69.0 1.0
OD1 B:ASP102 2.1 29.3 1.0
O B:HOH443 2.1 68.8 1.0
ND1 B:HIS156 2.2 31.2 1.0
NE2 B:HIS95 2.2 30.7 1.0
CG B:ASP102 2.9 38.3 1.0
OD2 B:ASP102 2.9 49.3 1.0
CE1 B:HIS156 3.0 38.4 1.0
CE1 B:HIS95 3.2 38.6 1.0
CD2 B:HIS95 3.3 32.1 1.0
N B:DAL202 3.3 64.8 1.0
CG B:HIS156 3.4 28.0 1.0
CA B:DAL202 3.6 53.1 1.0
CB B:HIS156 3.8 29.3 1.0
NE1 B:TRP155 4.1 43.6 1.0
NE2 B:HIS156 4.2 35.4 1.0
C B:DAL202 4.2 47.0 1.0
ND1 B:HIS95 4.3 29.6 1.0
CB B:ASP102 4.3 37.7 1.0
O B:HOH445 4.3 64.2 1.0
CD2 B:HIS156 4.4 34.1 1.0
NH2 B:ARG62 4.4 41.3 1.0
CG B:HIS95 4.4 37.9 1.0
OXT B:DAL202 4.4 49.3 1.0
OE1 B:GLU153 4.4 37.1 1.0
CD1 B:TRP155 4.5 40.9 1.0
CA B:HIS156 4.7 29.2 1.0
CA B:ASP102 4.8 29.7 1.0
N B:ASP102 4.9 30.0 1.0
CB B:DAL202 4.9 44.5 1.0
O B:ILE101 4.9 24.1 1.0
O B:DAL202 4.9 31.6 1.0

Reference:

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
Page generated: Wed Dec 16 05:36:06 2020

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