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Zinc in PDB 4ly4: Crystal Structure of Peptidoglycan Deacetylase (HP0310) with Zinc From Helicobacter Pylori

Protein crystallography data

The structure of Crystal Structure of Peptidoglycan Deacetylase (HP0310) with Zinc From Helicobacter Pylori, PDB code: 4ly4 was solved by M.M.Shaik, G.Zanotti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.48 / 2.20
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 113.640, 153.930, 153.880, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Peptidoglycan Deacetylase (HP0310) with Zinc From Helicobacter Pylori (pdb code 4ly4). 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 Peptidoglycan Deacetylase (HP0310) with Zinc From Helicobacter Pylori, PDB code: 4ly4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4ly4

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Zinc binding site 1 out of 4 in the Crystal Structure of Peptidoglycan Deacetylase (HP0310) with Zinc 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 Peptidoglycan Deacetylase (HP0310) with Zinc From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:34.2
occ:1.00
OD1 A:ASP14 2.1 24.4 1.0
NE2 A:HIS90 2.2 24.3 1.0
NE2 A:HIS86 2.2 20.6 1.0
OD2 A:ASP14 2.6 18.3 1.0
CG A:ASP14 2.7 19.9 1.0
CD2 A:HIS90 3.1 16.8 1.0
CE1 A:HIS86 3.1 25.6 1.0
CE1 A:HIS90 3.2 21.3 1.0
CD2 A:HIS86 3.3 19.4 1.0
CB A:ASP12 3.7 20.8 1.0
NE2 A:HIS247 4.0 17.6 1.0
OD2 A:ASP12 4.1 24.9 1.0
CB A:ASP14 4.2 19.4 1.0
CD2 A:HIS247 4.2 17.6 1.0
ND1 A:HIS86 4.2 22.1 1.0
CG A:HIS90 4.3 21.0 1.0
CG A:ASP12 4.3 22.0 1.0
ND1 A:HIS90 4.3 21.1 1.0
CG A:HIS86 4.4 18.3 1.0
OH A:TYR23 4.5 28.7 1.0
O A:HOH401 4.5 34.1 1.0
N A:TRP127 4.6 23.9 1.0
CA A:PRO126 4.7 23.4 1.0
CA A:ASP14 4.7 20.2 1.0
CA A:ASP12 4.9 21.3 1.0
O A:ASP12 5.0 23.1 1.0

Zinc binding site 2 out of 4 in 4ly4

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Zinc binding site 2 out of 4 in the Crystal Structure of Peptidoglycan Deacetylase (HP0310) with Zinc 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 Peptidoglycan Deacetylase (HP0310) with Zinc From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:36.2
occ:1.00
NE2 B:HIS90 2.0 23.1 1.0
OD1 B:ASP14 2.2 14.7 1.0
NE2 B:HIS86 2.2 19.1 1.0
O B:HOH401 2.6 33.8 1.0
CE1 B:HIS90 2.8 23.2 1.0
CG B:ASP14 2.9 23.4 1.0
OD2 B:ASP14 3.0 19.5 1.0
CE1 B:HIS86 3.1 20.1 1.0
CD2 B:HIS90 3.2 19.3 1.0
CD2 B:HIS86 3.4 20.9 1.0
CB B:ASP12 3.8 14.7 1.0
OD2 B:ASP12 4.0 15.5 1.0
ND1 B:HIS90 4.0 19.0 1.0
NE2 B:HIS247 4.1 15.5 1.0
CG B:HIS90 4.2 19.0 1.0
ND1 B:HIS86 4.2 18.9 1.0
CG B:ASP12 4.3 19.8 1.0
CB B:ASP14 4.4 19.5 1.0
CG B:HIS86 4.4 20.3 1.0
CD2 B:HIS247 4.4 16.8 1.0
N B:TRP127 4.4 29.0 1.0
CA B:PRO126 4.5 26.3 1.0
OH B:TYR23 4.6 30.8 1.0
CA B:ASP14 4.9 20.0 1.0

Zinc binding site 3 out of 4 in 4ly4

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Zinc binding site 3 out of 4 in the Crystal Structure of Peptidoglycan Deacetylase (HP0310) with Zinc 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 Peptidoglycan Deacetylase (HP0310) with Zinc From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:38.8
occ:1.00
NE2 C:HIS90 2.0 18.9 1.0
NE2 C:HIS86 2.3 17.0 1.0
OD1 C:ASP14 2.4 18.2 1.0
OD2 C:ASP14 2.9 18.1 1.0
CE1 C:HIS90 3.0 22.9 1.0
CG C:ASP14 3.0 18.5 1.0
CD2 C:HIS90 3.1 22.3 1.0
CD2 C:HIS86 3.2 19.4 1.0
CE1 C:HIS86 3.2 18.2 1.0
O C:HOH401 3.8 36.0 1.0
CB C:ASP12 3.9 21.6 1.0
OD2 C:ASP12 4.0 22.7 1.0
ND1 C:HIS90 4.1 21.1 1.0
CG C:HIS90 4.2 24.5 1.0
NE2 C:HIS247 4.2 17.3 1.0
OH C:TYR23 4.3 29.6 1.0
ND1 C:HIS86 4.3 17.6 1.0
N C:TRP127 4.3 23.1 1.0
CG C:ASP12 4.4 20.0 1.0
CG C:HIS86 4.4 19.0 1.0
CB C:ASP14 4.4 17.1 1.0
CD2 C:HIS247 4.5 15.9 1.0
CA C:PRO126 4.5 22.6 1.0
CA C:ASP14 5.0 18.4 1.0

Zinc binding site 4 out of 4 in 4ly4

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Zinc binding site 4 out of 4 in the Crystal Structure of Peptidoglycan Deacetylase (HP0310) with Zinc 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 Peptidoglycan Deacetylase (HP0310) with Zinc From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:33.9
occ:1.00
OD1 D:ASP14 2.1 18.6 1.0
NE2 D:HIS90 2.1 16.8 1.0
NE2 D:HIS86 2.1 20.4 1.0
O D:HOH401 2.1 36.0 1.0
CG D:ASP14 2.8 21.8 1.0
OD2 D:ASP14 2.9 21.1 1.0
CD2 D:HIS90 2.9 19.3 1.0
CE1 D:HIS86 3.0 15.8 1.0
CE1 D:HIS90 3.2 19.3 1.0
CD2 D:HIS86 3.2 20.7 1.0
CB D:ASP12 3.8 19.4 1.0
ND1 D:HIS86 4.1 20.1 1.0
CG D:HIS90 4.1 19.0 1.0
NE2 D:HIS247 4.1 21.1 1.0
ND1 D:HIS90 4.2 18.0 1.0
OD2 D:ASP12 4.2 27.1 1.0
CB D:ASP14 4.2 22.9 1.0
CG D:HIS86 4.3 20.2 1.0
OH D:TYR23 4.4 22.3 1.0
CD2 D:HIS247 4.4 23.3 1.0
CG D:ASP12 4.4 22.6 1.0
N D:TRP127 4.6 21.4 1.0
CA D:PRO126 4.7 21.4 1.0
CA D:ASP14 4.7 20.6 1.0

Reference:

M.M.Shaik, N.Bhattacharjee, A.Bhattacharjee, M.J.Field, G.Zanotti. Characterization of the Divalent Metal Binding Site of Bacterial Polysaccharide Deacetylase Using Crystallography and Quantum Chemical Calculations. Proteins V. 82 1311 2014.
ISSN: ISSN 0887-3585
PubMed: 24346839
DOI: 10.1002/PROT.24497
Page generated: Wed Dec 16 05:33:53 2020

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