Zinc in PDB 2nyq: Structure of Vibrio Proteolyticus Aminopeptidase with A Bound Trp Fragment of Dlwcf

All present enzymatic activity of Structure of Vibrio Proteolyticus Aminopeptidase with A Bound Trp Fragment of Dlwcf:
3.4.11.10;

The structure of Structure of Vibrio Proteolyticus Aminopeptidase with A Bound Trp Fragment of Dlwcf, PDB code: 2nyq was solved by B.Bennett, A.Kumar, B.Narayanan, J.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	107.800, 107.800, 99.600, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 25.6

The binding sites of Zinc atom in the Structure of Vibrio Proteolyticus Aminopeptidase with A Bound Trp Fragment of Dlwcf (pdb code 2nyq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Vibrio Proteolyticus Aminopeptidase with A Bound Trp Fragment of Dlwcf, PDB code: 2nyq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Vibrio Proteolyticus Aminopeptidase with A Bound Trp Fragment of Dlwcf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Vibrio Proteolyticus Aminopeptidase with A Bound Trp Fragment of Dlwcf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:29.1 occ:1.00 NE2 A:HIS256 2.2 22.7 1.0 OD2 A:ASP117 2.3 29.8 1.0 OE1 A:GLU152 2.4 28.7 1.0 OE2 A:GLU152 2.5 29.7 1.0 CD A:GLU152 2.7 29.1 1.0 CD1 B:TRP294 2.9 59.2 1.0 CG A:ASP117 2.9 29.0 1.0 OD1 A:ASP117 2.9 24.3 1.0 C B:TRP294 3.1 56.8 1.0 CE1 A:HIS256 3.2 22.9 1.0 CD2 A:HIS256 3.2 21.4 1.0 ZN A:ZN301 3.2 28.3 1.0 NE1 B:TRP294 3.6 59.8 1.0 CG B:TRP294 3.7 58.6 1.0 CA B:TRP294 3.8 57.3 1.0 CB B:TRP294 3.9 57.6 1.0 O B:TRP294 4.0 56.2 1.0 CG A:GLU152 4.3 26.7 1.0 O A:HOH307 4.3 34.9 1.0 ND1 A:HIS256 4.3 24.7 1.0 CB A:ASP117 4.3 30.2 1.0 CG A:HIS256 4.3 23.3 1.0 OE1 A:GLU151 4.4 29.9 1.0 NE2 A:HIS97 4.5 22.0 1.0 CE1 A:HIS97 4.5 23.7 1.0 O A:HOH441 4.7 55.2 1.0 CE2 B:TRP294 4.7 58.4 1.0 CG2 A:THR101 4.8 31.2 1.0 CD2 B:TRP294 4.8 57.7 1.0

Zinc binding site 2 out of 2 in the Structure of Vibrio Proteolyticus Aminopeptidase with A Bound Trp Fragment of Dlwcf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Vibrio Proteolyticus Aminopeptidase with A Bound Trp Fragment of Dlwcf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:28.3 occ:1.00 NE2 A:HIS97 2.2 22.0 1.0 OD1 A:ASP179 2.2 17.3 1.0 OD1 A:ASP117 2.3 24.3 1.0 O A:HOH441 2.4 55.2 1.0 OD2 A:ASP179 2.4 21.1 1.0 CG A:ASP179 2.6 19.8 1.0 NE1 B:TRP294 3.1 59.8 1.0 CE1 A:HIS97 3.1 23.7 1.0 ZN A:ZN300 3.2 29.1 1.0 CD2 A:HIS97 3.3 21.3 1.0 CG A:ASP117 3.4 29.0 1.0 O B:TRP294 3.5 56.2 1.0 C B:TRP294 3.6 56.8 1.0 CD1 B:TRP294 3.6 59.2 1.0 CE2 B:TRP294 3.8 58.4 1.0 OE2 A:GLU152 3.9 29.7 1.0 OE1 A:GLU151 3.9 29.9 1.0 OD2 A:ASP117 3.9 29.8 1.0 CB A:ASP179 4.1 20.6 1.0 ND1 A:HIS97 4.2 24.9 1.0 CD A:GLU151 4.3 30.9 1.0 CZ2 B:TRP294 4.3 57.7 1.0 CG A:HIS97 4.3 21.9 1.0 OE2 A:GLU151 4.4 30.4 1.0 CD A:GLU152 4.4 29.1 1.0 OE1 A:GLU152 4.5 28.7 1.0 CG B:TRP294 4.6 58.6 1.0 CB A:ASP117 4.7 30.2 1.0 CD2 B:TRP294 4.7 57.7 1.0 C A:ASP117 4.7 32.3 1.0 CB A:ASP118 4.7 31.9 1.0 CA A:ASP117 4.8 30.5 1.0 OG A:SER228 4.8 27.0 1.0 CG A:ASP118 4.8 31.0 1.0 CG A:MET180 4.8 22.9 1.0 CA A:ASP179 4.9 20.3 1.0 N A:ASP118 4.9 33.8 1.0 O A:ASP117 4.9 29.0 1.0 OD1 A:ASP118 5.0 28.1 1.0

A.Kumar, B.Narayanan, J.-J.Kim, B.Bennett. Substrate Recognition By the Leucine Aminopeptidase From Vibrio Proteolyticus To Be Published.