Nickel in PDB 7vgb: Crystal Structure of Apo Prolyl Oligopeptidase From Microbulbifer Arenaceous

All present enzymatic activity of Crystal Structure of Apo Prolyl Oligopeptidase From Microbulbifer Arenaceous:
3.4.21.26;

The structure of Crystal Structure of Apo Prolyl Oligopeptidase From Microbulbifer Arenaceous, PDB code: 7vgb was solved by P.Huang, Z.Q.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.20 / 2.23
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.39, 125.395, 89.848, 90, 96.84, 90
R / Rfree (%)	15.2 / 20.7

The binding sites of Nickel atom in the Crystal Structure of Apo Prolyl Oligopeptidase From Microbulbifer Arenaceous (pdb code 7vgb). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Apo Prolyl Oligopeptidase From Microbulbifer Arenaceous, PDB code: 7vgb:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Apo Prolyl Oligopeptidase From Microbulbifer Arenaceous


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Apo Prolyl Oligopeptidase From Microbulbifer Arenaceous within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni811 b:80.7 occ:1.00 OH A:TYR113 3.5 20.9 1.0 N A:GLY135 4.3 46.2 1.0 CE2 A:TYR115 4.4 17.7 1.0 CZ A:TYR113 4.4 20.9 1.0 OH A:TYR101 4.5 19.8 1.0 CD2 A:TYR115 4.5 17.8 1.0 CE2 A:TYR113 4.5 18.9 1.0 CA A:ASP134 4.6 54.0 1.0 CE2 A:TYR126 4.6 32.2 1.0 CZ A:TYR115 4.6 17.0 1.0 CG A:TYR115 4.7 18.1 1.0 CZ A:TYR126 4.7 34.3 1.0 CD2 A:TYR126 4.8 28.0 1.0 O A:HOH909 4.8 36.9 1.0 CE1 A:TYR115 4.8 17.7 1.0 CD1 A:TYR115 4.8 17.8 1.0 CB A:ASP134 4.9 60.4 1.0 CG A:ASP134 4.9 69.1 1.0 OD1 A:ASP134 4.9 69.6 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Apo Prolyl Oligopeptidase From Microbulbifer Arenaceous


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Apo Prolyl Oligopeptidase From Microbulbifer Arenaceous within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni805 b:87.9 occ:1.00 OH B:TYR113 3.4 32.0 1.0 N B:GLY135 4.1 34.2 1.0 CD2 B:TYR115 4.3 18.8 1.0 CE2 B:TYR115 4.3 19.1 1.0 CZ B:TYR113 4.4 29.7 1.0 OH B:TYR101 4.4 34.1 1.0 CE2 B:TYR126 4.4 31.4 1.0 CE2 B:TYR113 4.4 26.5 1.0 CG B:TYR115 4.6 18.1 1.0 CZ B:TYR115 4.6 18.7 1.0 CD2 B:TYR126 4.6 28.5 1.0 CZ B:TYR126 4.7 32.3 1.0 CA B:ASP134 4.7 42.2 1.0 CA B:GLY135 4.8 36.6 1.0 OD1 B:ASP134 4.9 60.8 1.0 CE1 B:TYR115 4.9 19.2 1.0 CD1 B:TYR115 4.9 18.2 1.0 C B:ASP134 5.0 38.9 1.0 CE2 B:TYR101 5.0 31.0 1.0

P.Huang, A.Lv, Q.Yan, Z.Jiang, S.Yang. The Structure and Molecular Dynamics of Prolyl Oligopeptidase From Microbulbifer Arenaceous Provide Insights Into Catalytic and Regulatory Mechanisms. Acta Crystallogr D Struct V. 78 735 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35647921
DOI: 10.1107/S2059798322004247