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Zinc in PDB 5dyf: The Crystal Structure of Aminopeptidase N in Complex with N-Benzyl-1, 2-Diaminoethylphosphonic Acid

Enzymatic activity of The Crystal Structure of Aminopeptidase N in Complex with N-Benzyl-1, 2-Diaminoethylphosphonic Acid

All present enzymatic activity of The Crystal Structure of Aminopeptidase N in Complex with N-Benzyl-1, 2-Diaminoethylphosphonic Acid:
3.4.11.2;

Protein crystallography data

The structure of The Crystal Structure of Aminopeptidase N in Complex with N-Benzyl-1, 2-Diaminoethylphosphonic Acid, PDB code: 5dyf was solved by B.Nocek, A.Joachimiak, S.Vassiliou, L.Berlicki, A.Mucha, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.65 / 1.85
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 224.644, 224.644, 57.938, 90.00, 90.00, 120.00
R / Rfree (%) 14.6 / 17.4

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Aminopeptidase N in Complex with N-Benzyl-1, 2-Diaminoethylphosphonic Acid (pdb code 5dyf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the The Crystal Structure of Aminopeptidase N in Complex with N-Benzyl-1, 2-Diaminoethylphosphonic Acid, PDB code: 5dyf:

Zinc binding site 1 out of 1 in 5dyf

Go back to Zinc Binding Sites List in 5dyf
Zinc binding site 1 out of 1 in the The Crystal Structure of Aminopeptidase N in Complex with N-Benzyl-1, 2-Diaminoethylphosphonic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Aminopeptidase N in Complex with N-Benzyl-1, 2-Diaminoethylphosphonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:17.1
occ:0.89
 NE2 A:HIS297 2.0 14.0 1.0
OE1 A:GLU316 2.1 13.7 1.0
NE2 A:HIS293 2.1 15.5 1.0
O10 A:5HR912 2.1 17.6 0.8
O9 A:5HR912 2.3 23.3 0.8
P4 A:5HR912 2.6 19.8 0.8
CD A:GLU316 2.8 16.9 1.0
OE2 A:GLU316 2.8 17.0 1.0
CD2 A:HIS297 3.0 12.4 1.0
CD2 A:HIS293 3.0 16.1 1.0
CE1 A:HIS297 3.0 12.2 1.0
HD2 A:HIS293 3.1 19.3 1.0
HD2 A:HIS297 3.1 14.9 1.0
CE1 A:HIS293 3.2 17.0 1.0
HE1 A:HIS297 3.3 14.7 1.0
HE1 A:HIS293 3.4 20.4 1.0
HH A:TYR377 3.6 25.5 1.0
HE2 A:TYR377 3.6 23.2 1.0
N6 A:5HR912 3.6 11.2 0.8
C3 A:5HR912 3.8 18.9 0.8
O8 A:5HR912 3.9 18.3 0.8
HA A:GLU316 4.0 17.7 1.0
HG21 A:THR319 4.1 17.2 1.0
H62 A:5HR912 4.1 13.4 0.8
ND1 A:HIS297 4.1 11.8 1.0
CG A:HIS297 4.2 11.5 1.0
CG A:HIS293 4.2 15.6 1.0
HB A:THR319 4.2 17.5 1.0
OH A:TYR377 4.2 21.3 1.0
ND1 A:HIS293 4.2 17.6 1.0
CE2 A:TYR377 4.2 19.3 1.0
CG A:GLU316 4.3 12.8 1.0
OE1 A:GLU260 4.3 17.4 1.0
HZ2 A:LYS315 4.3 19.2 1.0
H31 A:5HR912 4.4 22.7 0.8
CZ A:TYR377 4.6 19.3 1.0
OE1 A:GLU294 4.6 23.0 1.0
HG3 A:GLU316 4.6 15.3 1.0
HG22 A:THR319 4.6 17.2 1.0
HZ3 A:LYS315 4.7 19.2 1.0
CG2 A:THR319 4.7 14.3 1.0
OE2 A:GLU294 4.7 27.1 1.0
H22 A:5HR912 4.7 35.2 0.8
HB3 A:GLU316 4.8 19.4 1.0
HG2 A:GLU316 4.8 15.3 1.0
CD A:GLU260 4.8 17.9 1.0
O A:HOH1055 4.8 33.3 1.0
OE2 A:GLU260 4.9 18.7 1.0
CA A:GLU316 4.9 14.8 1.0
O A:HOH1632 4.9 37.5 1.0
CB A:GLU316 4.9 16.2 1.0
CB A:THR319 4.9 14.6 1.0
NZ A:LYS315 4.9 16.0 1.0
C2 A:5HR912 4.9 29.4 0.8
HD1 A:HIS297 4.9 14.1 1.0
HG3 A:LYS315 5.0 18.9 1.0

Reference:

B.Nocek, A.Joachimiak, S.Vassiliou, L.Berlicki, A.Mucha, Midwest Center For Structural Genomics (Mcsg). The Crystal Structure of Aminopeptidase N in Complex with N-Benzyl-1,2-Diaminoethylphosphonic Acid To Be Published.
Page generated: Sun Oct 27 14:56:49 2024

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