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Zinc in PDB 4tsd: Crystal Structure of Helicobacter Pylori HP1029

Protein crystallography data

The structure of Crystal Structure of Helicobacter Pylori HP1029, PDB code: 4tsd was solved by F.Vallese, R.Percudani, G.Zanotti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.57 / 1.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.788, 77.490, 99.134, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Helicobacter Pylori HP1029 (pdb code 4tsd). 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 Helicobacter Pylori HP1029, PDB code: 4tsd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4tsd

Go back to Zinc Binding Sites List in 4tsd
Zinc binding site 1 out of 2 in the Crystal Structure of Helicobacter Pylori HP1029


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 Helicobacter Pylori HP1029 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:21.4
occ:1.00
OD2 B:ASP86 2.0 17.6 1.0
NE2 B:HIS81 2.0 17.1 1.0
NE2 B:HIS145 2.1 14.6 1.0
O B:HOH465 2.1 27.0 1.0
CD2 B:HIS81 3.0 15.7 1.0
CG B:ASP86 3.0 16.4 1.0
CE1 B:HIS145 3.0 14.6 1.0
CE1 B:HIS81 3.0 17.3 1.0
CD2 B:HIS145 3.1 15.9 1.0
OD1 B:ASP86 3.4 17.5 1.0
O B:HOH452 3.5 33.8 1.0
OE1 B:GLU79 3.8 38.9 1.0
O B:HOH466 3.9 35.4 1.0
NZ B:LYS168 3.9 16.6 1.0
NE2 B:GLN88 3.9 16.8 1.0
CD B:GLU79 3.9 25.5 1.0
ND1 B:HIS81 4.1 16.4 1.0
ND1 B:HIS145 4.2 14.1 1.0
CG B:HIS81 4.2 14.8 1.0
CG B:HIS145 4.2 16.1 1.0
CB B:ASP86 4.3 13.7 1.0
CG B:GLU79 4.3 18.6 1.0
OE2 B:GLU79 4.3 29.6 1.0
O B:HOH404 4.7 28.3 1.0

Zinc binding site 2 out of 2 in 4tsd

Go back to Zinc Binding Sites List in 4tsd
Zinc binding site 2 out of 2 in the Crystal Structure of Helicobacter Pylori HP1029


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 Helicobacter Pylori HP1029 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:20.8
occ:1.00
O A:HOH464 2.0 24.8 1.0
OD2 A:ASP86 2.0 16.2 1.0
NE2 A:HIS81 2.0 15.7 1.0
NE2 A:HIS145 2.0 15.0 1.0
CE1 A:HIS145 3.0 14.5 1.0
CG A:ASP86 3.0 13.9 1.0
CD2 A:HIS81 3.0 15.4 1.0
CE1 A:HIS81 3.0 14.6 1.0
CD2 A:HIS145 3.1 14.7 1.0
OD1 A:ASP86 3.4 16.0 1.0
O A:HOH465 3.6 24.6 1.0
NE2 A:GLN88 3.9 19.6 1.0
OE1 A:GLU79 4.0 32.6 1.0
NZ A:LYS168 4.0 15.3 1.0
CD A:GLU79 4.0 26.7 1.0
O A:HOH466 4.1 31.0 1.0
ND1 A:HIS145 4.1 14.2 1.0
ND1 A:HIS81 4.1 16.4 1.0
CG A:HIS81 4.2 15.7 1.0
CG A:HIS145 4.2 14.1 1.0
CB A:ASP86 4.3 13.5 1.0
OE2 A:GLU79 4.4 30.8 1.0
CG A:GLU79 4.4 19.5 1.0
O A:HOH409 4.7 36.3 1.0

Reference:

F.Vallese, R.Percudani, W.Fischer, G.Zanotti. The Crystal Structure of Helicobacter Pylori HP1029 Highlights the Functional Diversity of the Sialic Acid-Related DUF386 Family. Febs J. V. 282 3311 2015.
ISSN: ISSN 1742-464X
PubMed: 26096900
DOI: 10.1111/FEBS.13344
Page generated: Wed Dec 16 05:47:17 2020

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