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Zinc in PDB 3ked: Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid

Enzymatic activity of Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid

All present enzymatic activity of Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid:
3.4.11.2;

Protein crystallography data

The structure of Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid, PDB code: 3ked was solved by A.Addlagatta, R.Gumpena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.94 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.601, 120.601, 170.479, 90.00, 90.00, 120.00
R / Rfree (%) 15.4 / 19.8

Other elements in 3ked:

The structure of Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid (pdb code 3ked). 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 Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid, PDB code: 3ked:

Zinc binding site 1 out of 1 in 3ked

Go back to Zinc Binding Sites List in 3ked
Zinc binding site 1 out of 1 in the Crystal Structure of Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid


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 Aminopeptidase N in Complex with 2,4- Diaminobutyric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn875

b:22.5
occ:1.00
 OXT A:DAB880 1.8 29.8 1.0
NE2 A:HIS297 2.0 20.1 1.0
OE1 A:GLU320 2.0 19.4 1.0
NE2 A:HIS301 2.1 15.2 1.0
C A:DAB880 2.7 31.2 1.0
CD A:GLU320 2.8 21.3 1.0
OE2 A:GLU320 2.9 22.2 1.0
CD2 A:HIS297 2.9 18.4 1.0
CD2 A:HIS301 3.0 14.1 1.0
CE1 A:HIS297 3.0 24.6 1.0
O A:DAB880 3.0 33.4 1.0
CE1 A:HIS301 3.1 17.4 1.0
CE2 A:TYR381 3.9 17.2 1.0
ND A:DAB880 4.0 22.3 1.0
CG A:HIS297 4.1 20.0 1.0
ND1 A:HIS297 4.1 19.9 1.0
OH A:TYR381 4.1 23.6 1.0
CG A:HIS301 4.2 18.2 1.0
ND1 A:HIS301 4.2 18.3 1.0
CA A:DAB880 4.2 32.5 1.0
CG A:GLU320 4.2 18.2 1.0
CZ A:TYR381 4.4 22.2 1.0
CG2 A:THR323 4.5 17.6 1.0
OE1 A:GLU264 4.5 23.3 1.0
OE1 A:GLU298 4.5 25.0 1.0
CB A:THR323 4.7 21.3 1.0
CA A:GLU320 4.8 20.7 1.0
OE2 A:GLU264 4.8 25.8 1.0
CB A:GLU320 4.8 19.5 1.0
O1B A:MLA991 4.8 76.4 1.0
CG A:DAB880 4.9 33.1 1.0
CD A:GLU264 4.9 25.4 1.0
CD2 A:TYR381 4.9 16.6 1.0

Reference:

R.Gumpena, C.Kishor, R.J.Ganji, A.Addlagatta. Discovery of Alpha, Beta- and Alpha, Gamma-Diamino Acid Scaffolds For the Inhibition of M1 Family Aminopeptidases Chemmedchem V. 6 1971 2011.
ISSN: ISSN 1860-7179
PubMed: 22025387
DOI: 10.1002/CMDC.201100298
Page generated: Sat Oct 26 07:47:36 2024

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