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Zinc in PDB 1xry: Crystal Structure of Aeromonas Proteolytica Aminopeptidase in Complex with Bestatin

Enzymatic activity of Crystal Structure of Aeromonas Proteolytica Aminopeptidase in Complex with Bestatin

All present enzymatic activity of Crystal Structure of Aeromonas Proteolytica Aminopeptidase in Complex with Bestatin:
3.4.11.10;

Protein crystallography data

The structure of Crystal Structure of Aeromonas Proteolytica Aminopeptidase in Complex with Bestatin, PDB code: 1xry was solved by R.Gilboa, J.-M.Rondeau, S.Blumberg, C.Tarnus, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.69 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 107.390, 107.390, 103.060, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase in Complex with Bestatin (pdb code 1xry). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase in Complex with Bestatin, PDB code: 1xry:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1xry

Go back to Zinc Binding Sites List in 1xry
Zinc binding site 1 out of 2 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase in Complex with Bestatin


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 Aeromonas Proteolytica Aminopeptidase in Complex with Bestatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:16.0
occ:1.00
OD2 A:ASP117 2.1 15.2 1.0
OE1 A:GLU152 2.1 14.9 1.0
NE2 A:HIS256 2.1 17.2 1.0
O2 A:BES2001 2.2 12.2 1.0
O3 A:BES2001 2.3 13.0 1.0
OE2 A:GLU152 2.3 13.9 1.0
CD A:GLU152 2.5 12.8 1.0
C2 A:BES2001 2.9 12.0 1.0
C3 A:BES2001 2.9 12.9 1.0
CE1 A:HIS256 3.0 21.7 1.0
CG A:ASP117 3.1 15.5 1.0
CD2 A:HIS256 3.2 15.6 1.0
OD1 A:ASP117 3.4 15.3 1.0
C1 A:BES2001 3.5 14.6 1.0
ZN A:ZN1002 3.5 15.7 1.0
N2 A:BES2001 4.0 8.0 1.0
OE1 A:GLU151 4.0 13.2 1.0
CG A:GLU152 4.1 13.4 1.0
O A:HOH2009 4.1 13.6 1.0
ND1 A:HIS256 4.2 21.9 1.0
N1 A:BES2001 4.2 14.8 1.0
CG A:HIS256 4.3 19.2 1.0
O A:HOH2017 4.4 16.9 1.0
CB A:ASP117 4.5 13.8 1.0
CE1 A:HIS97 4.5 16.5 1.0
NE2 A:HIS97 4.6 13.6 1.0
CG2 A:THR101 4.8 15.4 1.0
C6 A:BES2001 4.9 15.7 1.0
CB A:GLU152 4.9 13.3 1.0
C4 A:BES2001 5.0 14.7 1.0

Zinc binding site 2 out of 2 in 1xry

Go back to Zinc Binding Sites List in 1xry
Zinc binding site 2 out of 2 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase in Complex with Bestatin


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 Aeromonas Proteolytica Aminopeptidase in Complex with Bestatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:15.7
occ:1.00
O2 A:BES2001 2.0 12.2 1.0
OD1 A:ASP117 2.0 15.3 1.0
NE2 A:HIS97 2.2 13.6 1.0
OD1 A:ASP179 2.2 13.2 1.0
N2 A:BES2001 2.3 8.0 1.0
OD2 A:ASP179 2.4 11.8 1.0
CG A:ASP179 2.6 10.1 1.0
C2 A:BES2001 2.8 12.0 1.0
CG A:ASP117 2.9 15.5 1.0
CE1 A:HIS97 3.0 16.5 1.0
C1 A:BES2001 3.1 14.6 1.0
CD2 A:HIS97 3.2 13.0 1.0
OD2 A:ASP117 3.3 15.2 1.0
ZN A:ZN1001 3.5 16.0 1.0
OE1 A:GLU151 3.8 13.2 1.0
OE1 A:GLU152 4.0 14.9 1.0
CB A:ASP179 4.1 11.0 1.0
CB A:ASP117 4.2 13.8 1.0
ND1 A:HIS97 4.2 16.0 1.0
C3 A:BES2001 4.2 12.9 1.0
CB A:ASP118 4.2 10.4 1.0
CD A:GLU151 4.2 13.8 1.0
C6 A:BES2001 4.3 15.7 1.0
OE2 A:GLU151 4.3 12.4 1.0
CG A:HIS97 4.3 12.7 1.0
CA A:ASP117 4.6 13.7 1.0
O3 A:BES2001 4.7 13.0 1.0
CG A:ASP118 4.7 13.2 1.0
CG A:MET180 4.7 14.8 1.0
OG A:SER228 4.7 11.6 1.0
CD A:GLU152 4.8 12.8 1.0
SD A:MET180 4.8 17.2 1.0
C A:ASP117 4.8 13.0 1.0
CA A:ASP179 4.9 12.2 1.0
N A:ASP118 5.0 10.4 1.0

Reference:

R.Gilboa, J.-M.Rondeau, S.Blumberg, C.Tarnus, G.Shoham. Interactions of Streptomyces Griseus Aminopeptidase and Aeromonas Proteolytica Aminopeptidase with Bestatin. Structural Analysis of Homologous Enzymes with Different Binding Modes. To Be Published.
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