Zinc in PDB 2c1g: Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda)

All present enzymatic activity of Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda):
3.5.1.33;

The structure of Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda), PDB code: 2c1g 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)	14.96 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.529, 78.439, 99.515, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.2

The binding sites of Zinc atom in the Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) (pdb code 2c1g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda), PDB code: 2c1g:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1465 b:19.6 occ:1.00 OD1 A:ASP276 2.0 19.1 1.0 NE2 A:HIS330 2.0 18.9 1.0 O A:HOH2176 2.1 23.1 1.0 NE2 A:HIS326 2.2 15.8 1.0 OXT A:ACT1464 2.3 24.3 1.0 O A:ACT1464 2.4 26.4 1.0 C A:ACT1464 2.7 28.4 1.0 CD2 A:HIS330 3.0 21.8 1.0 CG A:ASP276 3.0 19.4 1.0 CE1 A:HIS330 3.1 22.2 1.0 CD2 A:HIS326 3.1 17.6 1.0 CE1 A:HIS326 3.2 17.3 1.0 OD2 A:ASP276 3.3 23.7 1.0 CB A:ASP275 4.0 15.6 1.0 OD2 A:ASP275 4.1 17.6 1.0 CG A:HIS330 4.1 20.7 1.0 ND1 A:HIS330 4.2 19.8 1.0 CH3 A:ACT1464 4.2 24.9 1.0 ND1 A:HIS326 4.3 17.1 1.0 CG A:HIS326 4.3 15.2 1.0 NE2 A:HIS417 4.3 20.1 1.0 CB A:ASP276 4.5 19.3 1.0 CG A:ASP275 4.5 16.8 1.0 CD2 A:HIS417 4.5 17.9 1.0 N A:ASP276 4.7 17.0 1.0 CA A:PRO366 4.7 19.2 1.0 CA A:ASP276 4.9 18.5 1.0

Zinc binding site 2 out of 3 in the Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1466 b:25.0 occ:1.00 OE2 A:GLU146 1.7 35.5 1.0 O A:HOH2177 2.1 33.4 1.0 OE1 A:GLU144 2.2 21.0 1.0 OE2 A:GLU144 2.4 26.8 1.0 CD A:GLU144 2.6 23.1 1.0 CD A:GLU146 2.8 36.4 1.0 CG A:GLU146 3.5 34.5 1.0 OE1 A:GLU146 3.9 34.9 1.0 NE2 A:GLN133 3.9 28.6 1.0 CG A:GLU144 4.1 21.0 1.0 N A:GLU146 4.4 19.8 1.0 CB A:GLU146 4.4 31.5 1.0 O A:GLU144 4.6 22.0 1.0 CA A:THR145 4.8 19.1 1.0 C A:THR145 4.9 21.5 1.0 C A:GLU144 4.9 19.8 1.0

Zinc binding site 3 out of 3 in the Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Streptococcus Pneumoniae Peptidoglycan Deacetylase (Sppgda) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1467 b:66.1 occ:1.00 NE2 A:HIS455 2.2 31.6 1.0 CD2 A:HIS455 3.2 33.8 1.0 CE1 A:HIS455 3.2 34.0 1.0 OD1 A:ASP379 3.4 38.1 1.0 CG A:HIS455 4.3 33.6 1.0 ND1 A:HIS455 4.3 32.5 1.0 CG A:ASP379 4.6 39.9 1.0 CB A:ALA454 4.6 30.8 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