Zinc in PDB 3p24: Structure of Profragilysin-3 From Bacteroides Fragilis

All present enzymatic activity of Structure of Profragilysin-3 From Bacteroides Fragilis:
3.4.24.74;

The structure of Structure of Profragilysin-3 From Bacteroides Fragilis, PDB code: 3p24 was solved by T.Goulas, J.L.Arolas, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.740, 69.140, 158.910, 90.00, 91.57, 90.00
R / Rfree (%)	17 / 20.4

The binding sites of Zinc atom in the Structure of Profragilysin-3 From Bacteroides Fragilis (pdb code 3p24). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Profragilysin-3 From Bacteroides Fragilis, PDB code: 3p24:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Profragilysin-3 From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Profragilysin-3 From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:19.1 occ:1.00 NE2 A:HIS348 2.0 15.0 1.0 NE2 A:HIS358 2.0 18.0 1.0 NE2 A:HIS352 2.0 16.9 1.0 OD1 A:ASP194 2.2 28.4 1.0 OD2 A:ASP194 2.4 25.9 1.0 CG A:ASP194 2.6 24.7 1.0 CD2 A:HIS358 2.9 18.1 1.0 CE1 A:HIS348 3.0 17.9 1.0 CD2 A:HIS348 3.0 17.0 1.0 CE1 A:HIS352 3.0 18.4 1.0 CD2 A:HIS352 3.0 16.8 1.0 CE1 A:HIS358 3.0 21.5 1.0 ND1 A:HIS348 4.1 18.5 1.0 CG A:HIS358 4.1 20.3 1.0 CG A:HIS348 4.1 17.3 1.0 CB A:ASP194 4.1 25.9 1.0 ND1 A:HIS358 4.1 18.4 1.0 ND1 A:HIS352 4.1 15.9 1.0 CG A:HIS352 4.2 16.3 1.0 CG A:TYR191 4.2 34.2 1.0 CB A:TYR191 4.2 37.9 1.0 CD2 A:TYR195 4.4 27.6 1.0 CD1 A:TYR191 4.5 28.1 1.0 CD2 A:TYR191 4.5 32.4 1.0 CE A:MET366 4.6 17.2 1.0 O A:ASP194 4.8 24.0 1.0 OE1 A:GLU349 4.9 19.1 1.0 C A:ASP194 4.9 25.6 1.0 CA A:ASP194 4.9 26.8 1.0 CE2 A:TYR195 5.0 30.5 1.0 N A:ASP194 5.0 29.9 1.0

Zinc binding site 2 out of 4 in the Structure of Profragilysin-3 From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Profragilysin-3 From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn999 b:34.6 occ:1.00 NE2 B:HIS348 2.0 31.1 1.0 NE2 B:HIS352 2.0 30.5 1.0 NE2 B:HIS358 2.1 37.0 1.0 OD1 B:ASP194 2.2 51.2 1.0 OD2 B:ASP194 2.3 50.6 1.0 CG B:ASP194 2.6 48.0 1.0 CD2 B:HIS358 2.9 38.4 1.0 CE1 B:HIS352 3.0 32.6 1.0 CD2 B:HIS348 3.0 28.8 1.0 CE1 B:HIS348 3.0 31.5 1.0 CD2 B:HIS352 3.1 31.0 1.0 CE1 B:HIS358 3.1 40.5 1.0 CB B:TYR191 3.9 65.8 1.0 CG B:TYR191 4.1 61.6 1.0 CB B:ASP194 4.1 48.4 1.0 ND1 B:HIS352 4.1 30.6 1.0 CG B:HIS358 4.1 41.0 1.0 ND1 B:HIS348 4.1 29.1 1.0 CG B:HIS348 4.1 29.1 1.0 ND1 B:HIS358 4.1 40.9 1.0 CD1 B:TYR191 4.2 59.4 1.0 CG B:HIS352 4.2 29.4 1.0 CD2 B:TYR195 4.3 53.5 1.0 CE B:MET366 4.5 29.7 1.0 O B:ASP194 4.7 46.3 1.0 CE2 B:TYR195 4.7 57.0 1.0 CD2 B:TYR191 4.7 57.9 1.0 OE1 B:GLU349 4.8 36.9 1.0 C B:ASP194 4.9 49.7 1.0 O B:TYR191 4.9 71.3 1.0 CA B:ASP194 4.9 51.2 1.0 CE1 B:TYR191 4.9 55.7 1.0 CA B:TYR191 5.0 68.1 1.0

Zinc binding site 3 out of 4 in the Structure of Profragilysin-3 From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Profragilysin-3 From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn999 b:25.5 occ:1.00 NE2 C:HIS348 2.0 21.8 1.0 NE2 C:HIS358 2.0 25.6 1.0 NE2 C:HIS352 2.1 22.9 1.0 OD1 C:ASP194 2.2 37.0 1.0 OD2 C:ASP194 2.3 33.2 1.0 CG C:ASP194 2.5 32.2 1.0 CD2 C:HIS358 2.9 26.9 1.0 CD2 C:HIS348 2.9 23.8 1.0 CE1 C:HIS348 3.0 21.6 1.0 CE1 C:HIS358 3.0 28.8 1.0 CD2 C:HIS352 3.0 23.6 1.0 CE1 C:HIS352 3.1 26.8 1.0 CB C:TYR191 3.7 46.8 1.0 O C:TYR191 3.9 49.6 1.0 CB C:ASP194 4.1 33.9 1.0 CG C:HIS358 4.1 28.9 1.0 ND1 C:HIS358 4.1 28.8 1.0 CG C:HIS348 4.1 20.1 1.0 ND1 C:HIS348 4.1 21.2 1.0 CG C:TYR191 4.2 42.2 1.0 ND1 C:HIS352 4.2 22.6 1.0 CG C:HIS352 4.2 24.1 1.0 CD2 C:TYR195 4.5 41.2 1.0 CD1 C:TYR191 4.5 40.2 1.0 CE C:MET366 4.6 21.3 1.0 OE1 C:GLU349 4.7 25.5 1.0 C C:TYR191 4.7 49.3 1.0 CA C:TYR191 4.8 47.8 1.0 CA C:ASP194 4.8 36.4 1.0 CD2 C:TYR191 4.8 40.3 1.0 O C:ASP194 4.9 33.9 1.0 C C:ASP194 4.9 36.2 1.0 N C:ASP194 5.0 38.7 1.0

Zinc binding site 4 out of 4 in the Structure of Profragilysin-3 From Bacteroides Fragilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Profragilysin-3 From Bacteroides Fragilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn999 b:26.1 occ:1.00 NE2 D:HIS358 2.0 29.2 1.0 NE2 D:HIS352 2.0 21.9 1.0 NE2 D:HIS348 2.1 23.4 1.0 OD2 D:ASP194 2.1 36.2 1.0 OD1 D:ASP194 2.4 35.3 1.0 CG D:ASP194 2.6 32.1 1.0 CD2 D:HIS358 3.0 27.6 1.0 CD2 D:HIS348 3.0 22.5 1.0 CD2 D:HIS352 3.0 22.2 1.0 CE1 D:HIS358 3.0 31.9 1.0 CE1 D:HIS352 3.0 24.7 1.0 CE1 D:HIS348 3.1 24.0 1.0 O D:TYR191 3.9 58.5 1.0 CB D:TYR191 4.0 55.4 1.0 CB D:ASP194 4.1 32.9 1.0 ND1 D:HIS358 4.1 30.6 1.0 CG D:HIS358 4.1 31.3 1.0 ND1 D:HIS352 4.1 21.4 1.0 CG D:HIS352 4.1 23.2 1.0 CG D:HIS348 4.2 20.8 1.0 ND1 D:HIS348 4.2 22.2 1.0 CG D:TYR191 4.2 49.1 1.0 CD1 D:TYR191 4.4 44.4 1.0 CE D:MET366 4.6 24.7 1.0 CD2 D:TYR195 4.6 36.7 1.0 C D:TYR191 4.7 57.8 1.0 OE1 D:GLU349 4.8 25.7 1.0 CA D:TYR191 4.8 56.8 1.0 CD2 D:TYR191 4.9 46.1 1.0 O D:ASP194 4.9 30.4 1.0 OE2 D:GLU349 4.9 22.7 1.0 CA D:ASP194 5.0 34.8 1.0 C D:ASP194 5.0 32.9 1.0

T.Goulas, J.L.Arolas, F.X.Gomis-Ruth. Structure, Function and Latency Regulation of A Bacterial Enterotoxin Potentially Derived From A Mammalian Adamalysin/Adam Xenolog. Proc.Natl.Acad.Sci.Usa V. 108 1856 2011.
ISSN: ISSN 0027-8424
PubMed: 21233422
DOI: 10.1073/PNAS.1012173108