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Zinc in PDB 4s2r: Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site

Enzymatic activity of Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site

All present enzymatic activity of Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site:
3.4.11.9;

Protein crystallography data

The structure of Crystal Structure of X-Prolyl Aminopeptidase From Caenorhabditis Elegans: A Cytosolic Enzyme with A Di-Nuclear Active Site, PDB code: 4s2r 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) 38.87 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 141.377, 87.910, 114.764, 90.00, 115.92, 90.00
R / Rfree (%) 16.3 / 21.4

Zinc Binding Sites:

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 4s2r). 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: 4s2r:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4s2r

Go back to Zinc Binding Sites List in 4s2r
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:27.5
occ:1.00
OE2 P:GLU536 2.1 20.6 1.0
OD2 P:ASP424 2.1 22.7 1.0
NE2 P:HIS487 2.3 17.9 1.0
OE2 P:GLU522 2.4 31.2 1.0
CD P:GLU536 3.1 21.1 1.0
CD P:GLU522 3.1 35.0 1.0
ZN P:ZN702 3.1 29.9 1.0
CG P:ASP424 3.2 26.0 1.0
OE1 P:GLU522 3.2 35.9 1.0
CD2 P:HIS487 3.2 14.3 1.0
CE1 P:HIS487 3.3 19.7 1.0
OE1 P:GLU536 3.4 27.5 1.0
OD1 P:ASP424 3.8 19.9 1.0
OG1 P:THR520 4.0 22.2 1.0
CG2 P:THR520 4.0 15.3 1.0
O P:HOH1061 4.2 55.8 1.0
CB P:ASP424 4.3 15.4 1.0
CB P:THR520 4.4 20.3 1.0
CG P:HIS487 4.4 17.1 1.0
ND1 P:HIS487 4.4 16.1 1.0
CG P:GLU536 4.4 23.2 1.0
CG P:GLU522 4.5 21.5 1.0
NE2 P:HIS496 4.6 46.2 1.0

Zinc binding site 2 out of 4 in 4s2r

Go back to Zinc Binding Sites List in 4s2r
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:29.9
occ:1.00
OE1 P:GLU536 2.0 27.5 1.0
OD1 P:ASP424 2.2 19.9 1.0
OD1 P:ASP413 2.2 84.7 1.0
CG P:ASP424 2.8 26.0 1.0
OD2 P:ASP424 2.9 22.7 1.0
CD P:GLU536 2.9 21.1 1.0
CG P:ASP413 3.0 46.2 1.0
OD2 P:ASP413 3.1 24.4 1.0
ZN P:ZN701 3.1 27.5 1.0
OE2 P:GLU536 3.2 20.6 1.0
OG1 P:THR426 3.6 20.4 1.0
CZ P:PHE378 3.8 24.5 1.0
OE1 P:GLU522 4.0 35.9 1.0
CB P:ASP424 4.2 15.4 1.0
CE1 P:PHE378 4.3 23.4 1.0
CG P:GLU536 4.3 23.2 1.0
N P:VAL425 4.4 18.9 1.0
CB P:ASP413 4.5 16.4 1.0
CE2 P:PHE378 4.5 18.0 1.0
C P:ASP424 4.5 22.7 1.0
O P:VAL425 4.6 16.8 1.0
CA P:ASP424 4.7 17.2 1.0
C P:VAL425 4.7 18.0 1.0
CD P:GLU522 4.8 35.0 1.0
OE2 P:GLU522 4.8 31.2 1.0
N P:SER414 4.9 17.0 1.0
CA P:ASP413 4.9 16.4 1.0
CB P:GLU536 4.9 15.1 1.0
CB P:THR426 5.0 15.7 1.0

Zinc binding site 3 out of 4 in 4s2r

Go back to Zinc Binding Sites List in 4s2r
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:25.8
occ:1.00
OD1 Q:ASP413 2.0 21.6 1.0
OD1 Q:ASP424 2.0 22.3 1.0
OE1 Q:GLU536 2.1 22.5 1.0
CG Q:ASP413 2.7 27.5 1.0
OD2 Q:ASP413 2.7 21.7 1.0
CD Q:GLU536 2.9 16.9 1.0
CG Q:ASP424 2.9 17.1 1.0
OE2 Q:GLU536 3.1 20.1 1.0
OD2 Q:ASP424 3.1 22.1 1.0
ZN Q:ZN702 3.2 28.1 1.0
OG1 Q:THR426 3.5 20.2 1.0
CZ Q:PHE378 3.7 25.3 1.0
O Q:HOH1114 4.0 60.8 1.0
OE1 Q:GLU522 4.1 31.8 1.0
CB Q:ASP413 4.2 22.7 1.0
CE1 Q:PHE378 4.3 21.3 1.0
CB Q:ASP424 4.3 17.9 1.0
CG Q:GLU536 4.3 19.1 1.0
CE2 Q:PHE378 4.4 26.4 1.0
N Q:VAL425 4.4 22.2 1.0
O Q:VAL425 4.5 17.6 1.0
C Q:ASP424 4.5 23.9 1.0
C Q:VAL425 4.6 17.4 1.0
CA Q:ASP424 4.7 18.9 1.0
CD Q:GLU522 4.7 37.0 1.0
OE2 Q:GLU522 4.8 43.0 1.0
CA Q:ASP413 4.8 20.9 1.0
N Q:SER414 4.9 18.1 1.0
CB Q:GLU536 4.9 17.8 1.0
CB Q:THR426 4.9 17.0 1.0
N Q:THR426 4.9 17.6 1.0
CA Q:VAL425 5.0 17.3 1.0
C Q:ASP413 5.0 28.9 1.0

Zinc binding site 4 out of 4 in 4s2r

Go back to Zinc Binding Sites List in 4s2r
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:28.1
occ:1.00
OE2 Q:GLU536 2.1 20.1 1.0
NE2 Q:HIS487 2.2 20.2 1.0
OD2 Q:ASP424 2.2 22.1 1.0
OE2 Q:GLU522 2.3 43.0 1.0
CD Q:GLU522 3.1 37.0 1.0
CD2 Q:HIS487 3.1 16.0 1.0
CE1 Q:HIS487 3.2 21.6 1.0
CG Q:ASP424 3.2 17.1 1.0
CD Q:GLU536 3.2 16.9 1.0
OE1 Q:GLU522 3.2 31.8 1.0
ZN Q:ZN701 3.2 25.8 1.0
OD1 Q:ASP424 3.6 22.3 1.0
OE1 Q:GLU536 3.6 22.5 1.0
OG1 Q:THR520 4.0 20.8 1.0
CG2 Q:THR520 4.0 18.7 1.0
CG Q:HIS487 4.3 16.3 1.0
ND1 Q:HIS487 4.3 18.5 1.0
CB Q:THR520 4.3 24.0 1.0
CB Q:ASP424 4.4 17.9 1.0
NE2 Q:HIS496 4.4 40.5 1.0
O Q:HOH1114 4.5 60.8 1.0
CG Q:GLU522 4.5 27.4 1.0
CG Q:GLU536 4.5 19.1 1.0
CD2 Q:HIS496 4.7 38.7 1.0

Reference:

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
Page generated: Wed Dec 16 05:46:42 2020

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