Zinc in PDB 3qbu: Crystal Structure of Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori

The structure of Crystal Structure of Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori, PDB code: 3qbu was solved by M.M.Shaik, L.Cendron, R.Percudani, G.Zanotti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.54 / 2.57
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	154.560, 154.730, 158.680, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.5

The binding sites of Zinc atom in the Crystal Structure of Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori (pdb code 3qbu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori, PDB code: 3qbu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori


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 Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn294 b:26.2 occ:1.00 NE2 A:HIS90 2.1 20.4 1.0 O A:HOH295 2.1 32.8 1.0 NE2 A:HIS86 2.1 25.3 1.0 OD1 A:ASP14 2.2 31.7 1.0 O A:HOH686 2.8 19.4 1.0 CD2 A:HIS90 2.9 21.4 1.0 CG A:ASP14 2.9 25.2 1.0 CE1 A:HIS86 2.9 26.0 1.0 OD2 A:ASP14 3.0 28.2 1.0 CE1 A:HIS90 3.2 27.0 1.0 CD2 A:HIS86 3.2 27.4 1.0 CB A:ASP12 3.9 22.0 1.0 CG A:HIS90 4.1 23.5 1.0 ND1 A:HIS86 4.1 26.6 1.0 ND1 A:HIS90 4.2 20.7 1.0 NE2 A:HIS247 4.2 26.0 1.0 OD2 A:ASP12 4.2 37.2 1.0 CG A:HIS86 4.3 21.9 1.0 CB A:ASP14 4.3 23.3 1.0 O A:HOH737 4.4 33.5 1.0 CD2 A:HIS247 4.4 22.8 1.0 CG A:ASP12 4.4 30.8 1.0 N A:TRP127 4.5 33.8 1.0 OH A:TYR23 4.5 31.3 1.0 CA A:PRO126 4.7 31.2 1.0 CA A:ASP14 4.7 26.1 1.0 N A:ASP14 5.0 25.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori


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 Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn294 b:29.7 occ:1.00 OD1 B:ASP14 2.1 28.6 1.0 NE2 B:HIS86 2.2 24.8 1.0 NE2 B:HIS90 2.2 19.2 1.0 O B:HOH759 2.4 15.6 1.0 CG B:ASP14 2.8 24.4 1.0 OD2 B:ASP14 2.9 28.5 1.0 CE1 B:HIS86 3.0 24.7 1.0 CD2 B:HIS90 3.1 22.4 1.0 CD2 B:HIS86 3.3 27.5 1.0 CE1 B:HIS90 3.3 25.1 1.0 O B:HOH690 3.4 37.3 1.0 CB B:ASP12 3.7 20.8 1.0 NE2 B:HIS247 4.0 25.1 1.0 OD2 B:ASP12 4.1 36.8 1.0 CD2 B:HIS247 4.2 22.5 1.0 ND1 B:HIS86 4.2 27.9 1.0 CB B:ASP14 4.2 20.7 1.0 O B:HOH791 4.3 34.3 1.0 CG B:HIS90 4.3 21.8 1.0 CG B:ASP12 4.3 32.5 1.0 CG B:HIS86 4.4 23.7 1.0 ND1 B:HIS90 4.4 21.4 1.0 OH B:TYR23 4.5 33.2 1.0 O B:HOH767 4.6 35.9 1.0 N B:TRP127 4.6 34.5 1.0 CA B:ASP14 4.7 26.4 1.0 N B:ASP14 4.9 25.4 1.0 CA B:PRO126 4.9 30.0 1.0 CA B:ASP12 4.9 24.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn294 b:29.8 occ:1.00 NE2 C:HIS90 2.1 19.2 1.0 OD1 C:ASP14 2.2 30.4 1.0 NE2 C:HIS86 2.2 24.8 1.0 O C:HOH386 2.3 22.8 1.0 O C:HOH689 2.4 15.3 1.0 CG C:ASP14 2.8 26.4 1.0 OD2 C:ASP14 2.9 30.7 1.0 CD2 C:HIS90 2.9 22.6 1.0 CE1 C:HIS86 3.1 25.4 1.0 CE1 C:HIS90 3.2 25.5 1.0 CD2 C:HIS86 3.3 28.3 1.0 CB C:ASP12 3.9 23.4 1.0 NE2 C:HIS247 4.1 25.5 1.0 CG C:HIS90 4.1 21.5 1.0 ND1 C:HIS90 4.2 19.8 1.0 CB C:ASP14 4.2 22.2 1.0 ND1 C:HIS86 4.2 27.5 1.0 OD2 C:ASP12 4.3 35.4 1.0 CD2 C:HIS247 4.3 25.4 1.0 CG C:HIS86 4.4 24.3 1.0 OH C:TYR23 4.4 29.8 1.0 CG C:ASP12 4.4 30.8 1.0 O C:HOH725 4.5 30.4 1.0 N C:TRP127 4.5 35.9 1.0 O C:HOH760 4.5 28.9 1.0 CA C:ASP14 4.7 25.5 1.0 CA C:PRO126 4.8 30.7 1.0 N C:ASP14 4.9 24.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Putative Peptidoglycan Deactelyase (HP0310) From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn294 b:28.1 occ:1.00 OD1 D:ASP14 2.1 29.4 1.0 NE2 D:HIS90 2.1 18.0 1.0 NE2 D:HIS86 2.3 22.4 1.0 O D:HOH429 2.7 20.8 1.0 CG D:ASP14 2.7 27.6 1.0 OD2 D:ASP14 2.7 28.0 1.0 CD2 D:HIS90 3.0 24.3 1.0 CE1 D:HIS86 3.2 24.9 1.0 CE1 D:HIS90 3.2 25.3 1.0 CD2 D:HIS86 3.4 27.6 1.0 CB D:ASP12 3.9 23.9 1.0 NE2 D:HIS247 4.0 25.6 1.0 CB D:ASP14 4.2 22.6 1.0 CD2 D:HIS247 4.2 24.7 1.0 CG D:HIS90 4.2 22.2 1.0 OD2 D:ASP12 4.2 37.5 1.0 ND1 D:HIS90 4.3 22.2 1.0 OH D:TYR23 4.3 27.2 1.0 ND1 D:HIS86 4.4 29.5 1.0 CG D:ASP12 4.4 31.0 1.0 CG D:HIS86 4.5 22.9 1.0 N D:TRP127 4.6 34.4 1.0 O D:HOH822 4.6 41.5 1.0 CA D:ASP14 4.7 26.2 1.0 O D:HOH734 4.8 33.9 1.0 N D:ASP14 4.9 22.8 1.0 CA D:PRO126 4.9 30.9 1.0

M.M.Shaik, L.Cendron, R.Percudani, G.Zanotti. The Structure of Helicobacter Pylori HP0310 Reveals An Atypical Peptidoglycan Deacetylase. Plos One V. 6 19207 2011.
ISSN: ESSN 1932-6203
PubMed: 21559431
DOI: 10.1371/JOURNAL.PONE.0019207