Zinc in PDB 2c1i: Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) D 275 N Mutant.

All present enzymatic activity of Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) D 275 N Mutant.:
3.5.1.33;

The structure of Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) D 275 N Mutant., PDB code: 2c1i was solved by D.E.Blair, A.W.Schuttelkopf, J.I.Macrae, D.M.F.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.275, 79.239, 100.377, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.5

The binding sites of Zinc atom in the Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) D 275 N Mutant. (pdb code 2c1i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) D 275 N Mutant., PDB code: 2c1i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) D 275 N Mutant.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) D 275 N Mutant. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1465 b:14.0 occ:1.00 OD1 A:ASP276 1.9 16.7 1.0 O3 A:SO41467 1.9 14.6 1.0 NE2 A:HIS330 2.0 14.3 1.0 NE2 A:HIS326 2.0 13.1 1.0 CD2 A:HIS330 2.9 15.1 1.0 CG A:ASP276 2.9 14.5 1.0 CD2 A:HIS326 3.0 13.2 1.0 S A:SO41467 3.0 15.1 1.0 CE1 A:HIS326 3.1 13.9 1.0 CE1 A:HIS330 3.1 14.3 1.0 OD2 A:ASP276 3.2 18.7 1.0 O1 A:SO41467 3.3 16.5 1.0 O A:HOH2211 3.6 22.2 1.0 O2 A:SO41467 3.6 17.9 1.0 ND2 A:ASN275 3.8 13.2 1.0 CB A:ASN275 4.0 12.2 1.0 CG A:HIS330 4.1 14.4 1.0 CG A:HIS326 4.2 12.1 1.0 ND1 A:HIS330 4.2 15.0 1.0 ND1 A:HIS326 4.2 12.5 1.0 O4 A:SO41467 4.2 16.4 1.0 CB A:ASP276 4.3 14.0 1.0 CG A:ASN275 4.3 12.6 1.0 O A:HOH2210 4.7 14.6 1.0 N A:ASP276 4.7 12.8 1.0 CA A:ASP276 4.7 13.7 1.0 CD2 A:HIS417 4.7 15.1 1.0 CA A:PRO366 4.8 13.6 1.0 NE2 A:HIS417 4.9 15.6 1.0 CB A:PRO366 4.9 13.9 1.0 C A:ASN275 5.0 12.6 1.0

Zinc binding site 2 out of 2 in the Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) D 275 N Mutant.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) D 275 N Mutant. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1466 b:16.9 occ:1.00 OE2 A:GLU146 1.9 22.1 1.0 O A:HOH2209 2.0 22.8 1.0 OE1 A:GLU144 2.2 16.2 1.0 OE2 A:GLU144 2.4 16.4 1.0 CD A:GLU144 2.6 15.4 1.0 CD A:GLU146 3.0 23.6 1.0 CG A:GLU146 3.4 23.0 1.0 OE1 A:GLU146 4.1 23.3 1.0 CG A:GLU144 4.1 15.2 1.0 NE2 A:GLN133 4.1 17.3 1.0 CB A:GLU146 4.3 20.9 1.0 N A:GLU146 4.3 15.3 1.0 O A:GLU144 4.6 12.5 1.0 O A:HOH2057 4.8 24.0 1.0 C A:THR145 4.8 14.6 1.0 CA A:THR145 4.9 14.1 1.0 C A:GLU144 4.9 12.5 1.0 CA A:GLU146 5.0 17.6 1.0

D.E.Blair, A.W.Schuttelkopf, J.I.Macrae, D.M.Van Aalten. Structure and Metal-Dependent Mechanism of Peptidoglycan Deacetylase, A Streptococcal Virulence Factor. Proc. Natl. Acad. Sci. V. 102 15429 2005U.S.A..
ISSN: ISSN 0027-8424
PubMed: 16221761
DOI: 10.1073/PNAS.0504339102