Zinc in PDB 4nrn: Crystal Structure of Metal-Bound Toxin From Helicobacter Pylori

The structure of Crystal Structure of Metal-Bound Toxin From Helicobacter Pylori, PDB code: 4nrn was solved by B.J.Lee, H.Im, C.Pathak, S.B.Jang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.88 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.012, 47.028, 52.599, 90.00, 110.01, 90.00
R / Rfree (%)	18 / 22.6

The binding sites of Zinc atom in the Crystal Structure of Metal-Bound Toxin From Helicobacter Pylori (pdb code 4nrn). 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 Metal-Bound Toxin From Helicobacter Pylori, PDB code: 4nrn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Metal-Bound Toxin 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 Metal-Bound Toxin From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:38.9 occ:1.00 NE2 A:HIS60 2.0 39.3 1.0 NE2 A:HIS47 2.3 20.0 1.0 OE2 A:GLU58 2.4 23.9 1.0 O A:HOH249 2.6 34.2 1.0 ZN A:ZN102 2.9 45.4 1.0 CE1 A:HIS60 3.0 42.9 1.0 CD2 A:HIS60 3.0 43.3 1.0 CE1 A:HIS47 3.2 22.9 1.0 CD2 A:HIS47 3.3 18.2 1.0 CD A:GLU58 3.5 32.4 1.0 ND1 A:HIS60 4.1 45.8 1.0 CG A:GLU58 4.1 30.4 1.0 CG A:HIS60 4.1 41.0 1.0 O A:HOH254 4.2 50.5 1.0 ND1 A:HIS47 4.3 18.9 1.0 CG A:HIS47 4.4 14.0 1.0 NE2 A:HIS86 4.4 39.6 1.0 OE1 A:GLU58 4.5 37.8 1.0 CB A:GLU58 4.6 27.0 1.0 CD2 A:LEU66 4.8 22.3 1.0 O A:HOH230 4.9 42.5 1.0 CE1 A:HIS86 5.0 38.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Metal-Bound Toxin 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 Metal-Bound Toxin From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:45.4 occ:1.00 O A:HOH230 2.4 42.5 1.0 NE2 A:HIS86 2.5 39.6 1.0 OE2 A:GLU58 2.7 23.9 1.0 ZN A:ZN101 2.9 38.9 1.0 CD2 A:HIS86 3.3 39.1 1.0 CD A:GLU58 3.6 32.4 1.0 CE1 A:HIS86 3.6 38.1 1.0 OE1 A:GLU58 3.8 37.8 1.0 NE2 A:HIS60 4.2 39.3 1.0 NE2 A:HIS47 4.3 20.0 1.0 CE1 A:HIS47 4.4 22.9 1.0 O A:HOH249 4.4 34.2 1.0 CE1 A:HIS60 4.4 42.9 1.0 CG A:HIS86 4.5 36.8 1.0 ND1 A:HIS86 4.6 38.0 1.0 CD1 A:LEU66 4.7 19.0 1.0 CG A:GLU58 4.9 30.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Metal-Bound Toxin 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 Metal-Bound Toxin From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:34.5 occ:1.00 NE2 B:HIS47 2.1 22.9 1.0 NE2 B:HIS60 2.2 36.0 1.0 O B:HOH235 2.4 32.3 1.0 OE2 B:GLU58 2.5 37.4 1.0 CE1 B:HIS60 2.8 38.5 1.0 CD2 B:HIS47 3.1 23.4 1.0 CE1 B:HIS47 3.1 23.5 1.0 ZN B:ZN102 3.3 39.0 1.0 CD B:GLU58 3.4 38.9 1.0 CD2 B:HIS60 3.4 30.1 1.0 CG B:GLU58 4.0 27.7 1.0 ND1 B:HIS60 4.0 36.3 1.0 ND1 B:HIS47 4.2 26.3 1.0 CG B:HIS47 4.2 25.1 1.0 OE1 B:GLU58 4.3 49.5 1.0 NE2 B:HIS86 4.4 64.3 1.0 CG B:HIS60 4.4 26.0 1.0 CE1 B:HIS86 5.0 64.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Metal-Bound Toxin 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 Metal-Bound Toxin From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:39.0 occ:1.00 OE2 B:GLU58 2.5 37.4 1.0 NE2 B:HIS86 2.8 64.3 1.0 OE1 B:GLU58 3.0 49.5 1.0 CD B:GLU58 3.1 38.9 1.0 CD2 B:HIS86 3.1 61.1 1.0 ZN B:ZN101 3.3 34.5 1.0 O B:HOH249 3.7 66.6 1.0 CE1 B:HIS86 4.0 64.4 1.0 O B:HOH232 4.3 23.4 1.0 CE1 B:HIS47 4.3 23.5 1.0 NE2 B:HIS47 4.4 22.9 1.0 CG B:HIS86 4.4 57.3 1.0 CD1 B:LEU66 4.4 22.4 1.0 CG B:GLU58 4.5 27.7 1.0 CE2 B:PHE90 4.6 77.4 1.0 CE1 B:HIS60 4.7 38.5 1.0 NE2 B:HIS60 4.7 36.0 1.0 ND1 B:HIS86 4.8 60.4 1.0 CD2 B:LEU49 4.8 43.1 1.0 CZ B:PHE90 4.9 78.6 1.0 CD2 B:LEU66 5.0 24.5 1.0

H.Im, S.B.Jang, C.Pathak, Y.J.Yang, H.J.Yoon, T.K.Yu, J.Y.Suh, B.J.Lee. Crystal Structure of Toxin HP0892 From Helicobacter Pylori with Two Zn(II) at 1.8 Angstrom Resolution Protein Sci. V. 23 819 2014.
ISSN: ISSN 0961-8368
PubMed: 24677509
DOI: 10.1002/PRO.2465