Zinc in PDB 4s2t: Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site

The structure of Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site, PDB code: 4s2t was solved by S.Iyer, P.La-Borde, K.A.P.Payne, M.R.Parsons, A.J.Turner, R.E.Isaac, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.52 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.590, 86.810, 113.130, 90.00, 115.96, 90.00
R / Rfree (%)	20.5 / 24.7

The binding sites of Zinc atom in the Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site (pdb code 4s2t). 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 X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site, PDB code: 4s2t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site


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 X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn701 b:47.5 occ:1.00 OD1 P:ASP424 2.1 36.5 1.0 OE1 P:GLU536 2.1 32.6 1.0 O2 A:01B1 2.2 39.7 0.5 OD1 P:ASP413 2.3 27.4 1.0 N2 A:01B1 2.7 46.0 0.5 OD2 P:ASP413 2.7 28.5 1.0 CG P:ASP413 2.8 26.7 1.0 CG P:ASP424 2.9 32.5 1.0 CD P:GLU536 3.0 30.6 1.0 ZN P:ZN702 3.0 55.2 1.0 OD2 P:ASP424 3.1 35.2 1.0 C2 A:01B1 3.2 43.1 0.5 OE2 P:GLU536 3.2 31.1 1.0 C1 A:01B1 3.4 45.2 0.5 OG1 P:THR426 3.5 23.6 1.0 CZ P:PHE378 3.7 30.6 1.0 OE1 P:GLU522 4.0 36.6 1.0 CB P:ASP413 4.3 27.3 1.0 CE1 P:PHE378 4.3 30.8 1.0 CB P:ASP424 4.3 30.2 1.0 CE2 P:PHE378 4.4 29.6 1.0 CG P:GLU536 4.4 27.8 1.0 N P:VAL425 4.4 27.6 1.0 C3 A:01B1 4.5 41.9 0.5 C12 A:01B1 4.5 44.8 0.5 O P:VAL425 4.6 25.4 1.0 C P:ASP424 4.7 27.9 1.0 C P:VAL425 4.7 25.2 1.0 CA P:ASP424 4.8 27.1 1.0 C6 A:01B1 4.8 46.0 0.5 C7 A:01B1 4.8 46.2 0.5 CD P:GLU522 4.9 32.2 1.0 CB P:THR426 4.9 22.7 1.0 CB P:GLU536 4.9 26.5 1.0 CA P:ASP413 4.9 25.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site


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 X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn702 b:55.2 occ:1.00 O2 A:01B1 2.0 39.7 0.5 OE2 P:GLU536 2.0 31.1 1.0 OD2 P:ASP424 2.2 35.2 1.0 NE2 P:HIS487 2.6 28.5 1.0 OE2 P:GLU522 2.7 33.3 1.0 C2 A:01B1 2.7 43.1 0.5 C1 A:01B1 2.8 45.2 0.5 ZN P:ZN701 3.0 47.5 1.0 CD P:GLU536 3.1 30.6 1.0 O3 A:01B1 3.1 44.6 0.5 OE1 P:GLU522 3.1 36.6 1.0 N2 A:01B1 3.1 46.0 0.5 C3 A:01B1 3.1 41.9 0.5 CG P:ASP424 3.2 32.5 1.0 CD P:GLU522 3.2 32.2 1.0 OE1 P:GLU536 3.4 32.6 1.0 CE1 P:HIS487 3.4 29.2 1.0 CD2 P:HIS487 3.6 27.7 1.0 OD1 P:ASP424 3.6 36.5 1.0 CG2 P:THR520 4.1 27.4 1.0 OG1 P:THR520 4.2 28.5 1.0 N A:PRO2 4.2 39.4 0.5 C6 A:01B1 4.3 46.0 0.5 CB P:ASP424 4.4 30.2 1.0 CG P:GLU536 4.4 27.8 1.0 CB P:THR520 4.4 25.6 1.0 NE2 P:HIS496 4.5 47.2 1.0 CG P:GLU522 4.6 27.6 1.0 ND1 P:HIS487 4.6 28.5 1.0 CG P:HIS487 4.7 28.1 1.0 CD2 P:HIS496 4.9 45.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site


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 X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site within 5.0Å range: probe atom residue distance (Å) B Occ Q:Zn701 b:48.9 occ:1.00 OE1 Q:GLU536 2.1 25.9 1.0 OD1 Q:ASP424 2.1 31.3 1.0 O2 B:01B1 2.1 40.4 0.5 OD1 Q:ASP413 2.2 26.6 1.0 OD2 Q:ASP413 2.7 24.5 1.0 CG Q:ASP413 2.8 24.6 1.0 CG Q:ASP424 2.9 29.1 1.0 N2 B:01B1 2.9 43.2 0.5 CD Q:GLU536 3.0 24.7 1.0 ZN Q:ZN702 3.1 48.2 1.0 OD2 Q:ASP424 3.1 29.4 1.0 OE2 Q:GLU536 3.2 24.4 1.0 C2 B:01B1 3.2 41.5 0.5 OG1 Q:THR426 3.5 22.4 1.0 C1 B:01B1 3.6 43.3 0.5 CZ Q:PHE378 3.7 30.0 1.0 OE1 Q:GLU522 4.0 38.9 1.0 CB Q:ASP413 4.3 24.5 1.0 CB Q:ASP424 4.3 27.3 1.0 CE1 Q:PHE378 4.3 31.2 1.0 N Q:VAL425 4.4 25.6 1.0 CG Q:GLU536 4.4 23.6 1.0 CE2 Q:PHE378 4.4 30.4 1.0 C3 B:01B1 4.5 38.3 0.5 O Q:VAL425 4.5 21.7 1.0 C12 B:01B1 4.6 52.5 0.5 C Q:ASP424 4.6 27.1 1.0 C Q:VAL425 4.6 24.3 1.0 CA Q:ASP424 4.7 25.8 1.0 CB Q:THR426 4.8 23.8 1.0 CA Q:ASP413 4.9 23.6 1.0 CB Q:GLU536 4.9 22.9 1.0 CD Q:GLU522 4.9 32.3 1.0 N Q:SER414 4.9 23.6 1.0 C6 B:01B1 4.9 48.2 0.5 CA Q:VAL425 5.0 25.1 1.0 N Q:THR426 5.0 23.6 1.0 C7 B:01B1 5.0 51.3 0.5 CD B:PRO2 5.0 32.0 0.5

Zinc binding site 4 out of 4 in the Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site


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 X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site within 5.0Å range: probe atom residue distance (Å) B Occ Q:Zn702 b:48.2 occ:1.00 O2 B:01B1 2.0 40.4 0.5 OE2 Q:GLU536 2.1 24.4 1.0 OD2 Q:ASP424 2.1 29.4 1.0 NE2 Q:HIS487 2.5 26.8 1.0 OE2 Q:GLU522 2.7 37.1 1.0 C2 B:01B1 2.7 41.5 0.5 C1 B:01B1 2.9 43.3 0.5 O3 B:01B1 3.1 40.4 0.5 C3 B:01B1 3.1 38.3 0.5 ZN Q:ZN701 3.1 48.9 1.0 CG Q:ASP424 3.1 29.1 1.0 CD Q:GLU536 3.1 24.7 1.0 OE1 Q:GLU522 3.2 38.9 1.0 N2 B:01B1 3.2 43.2 0.5 CD Q:GLU522 3.3 32.3 1.0 CE1 Q:HIS487 3.3 27.8 1.0 OE1 Q:GLU536 3.5 25.9 1.0 OD1 Q:ASP424 3.5 31.3 1.0 CD2 Q:HIS487 3.6 26.2 1.0 CG2 Q:THR520 4.0 23.7 1.0 N B:PRO2 4.1 33.2 0.5 OG1 Q:THR520 4.2 25.1 1.0 CB Q:ASP424 4.3 27.3 1.0 C6 B:01B1 4.4 48.2 0.5 CB Q:THR520 4.4 23.5 1.0 NE2 Q:HIS496 4.4 45.4 1.0 CG Q:GLU536 4.4 23.6 1.0 ND1 Q:HIS487 4.5 28.1 1.0 CG Q:HIS487 4.6 25.2 1.0 CG Q:GLU522 4.6 28.1 1.0 CD2 Q:HIS496 4.8 44.4 1.0 CD B:PRO2 4.8 32.0 0.5

S.Iyer, P.J.La-Borde, K.A.Payne, M.R.Parsons, A.J.Turner, R.E.Isaac, K.R.Acharya. Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site. Febs Open Bio V. 5 292 2015.
ISSN: ESSN 2211-5463
PubMed: 25905034
DOI: 10.1016/J.FOB.2015.03.013