Zinc in PDB 4dyo: Crystal Structure of Human Aspartyl Aminopeptidase (Dnpep) in Complex with Aspartic Acid Hydroxamate

All present enzymatic activity of Crystal Structure of Human Aspartyl Aminopeptidase (Dnpep) in Complex with Aspartic Acid Hydroxamate:
3.4.11.21;

The structure of Crystal Structure of Human Aspartyl Aminopeptidase (Dnpep) in Complex with Aspartic Acid Hydroxamate, PDB code: 4dyo was solved by A.Chaikuad, E.Pilka, M.Vollmar, T.Krojer, J.R.C.Muniz, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, K.L.Kavanagh, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.69 / 2.20
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	244.595, 244.595, 244.595, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 19.5

The structure of Crystal Structure of Human Aspartyl Aminopeptidase (Dnpep) in Complex with Aspartic Acid Hydroxamate also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Human Aspartyl Aminopeptidase (Dnpep) in Complex with Aspartic Acid Hydroxamate (pdb code 4dyo). 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 Human Aspartyl Aminopeptidase (Dnpep) in Complex with Aspartic Acid Hydroxamate, PDB code: 4dyo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Aspartyl Aminopeptidase (Dnpep) in Complex with Aspartic Acid Hydroxamate


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 Human Aspartyl Aminopeptidase (Dnpep) in Complex with Aspartic Acid Hydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:27.4 occ:1.00 OD2 A:ASP264 2.0 12.4 1.0 OE1 A:GLU302 2.0 22.0 1.0 NE2 A:HIS440 2.1 15.4 1.0 OD1 A:SD4504 2.2 23.8 1.0 OAD A:SD4504 2.2 28.3 1.0 OE2 A:GLU302 2.6 12.8 1.0 CD A:GLU302 2.6 15.6 1.0 CG A:SD4504 2.9 22.9 1.0 ND2 A:SD4504 3.0 19.6 1.0 CG A:ASP264 3.0 20.2 1.0 CD2 A:HIS440 3.0 13.7 1.0 CE1 A:HIS440 3.2 15.9 1.0 OD1 A:ASP264 3.4 21.7 1.0 ZN A:ZN502 3.4 28.1 1.0 CG A:GLU302 4.1 16.4 1.0 CG A:HIS440 4.2 16.1 1.0 ND1 A:HIS440 4.3 12.8 1.0 OE1 A:GLU301 4.3 22.5 1.0 CB A:ASP264 4.4 16.7 1.0 CB A:SD4504 4.4 29.0 1.0 CE1 A:HIS94 4.5 7.5 1.0 NE2 A:HIS94 4.6 12.4 1.0 SD A:MET439 4.6 19.2 1.0 CD A:PRO98 4.7 15.0 1.0 CG A:MET439 4.8 24.1 1.0 CG A:PRO98 4.8 20.8 1.0 O A:HOH670 4.9 14.7 1.0 CA A:SD4504 5.0 36.2 1.0 O A:HOH747 5.0 53.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Aspartyl Aminopeptidase (Dnpep) in Complex with Aspartic Acid Hydroxamate


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 Human Aspartyl Aminopeptidase (Dnpep) in Complex with Aspartic Acid Hydroxamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:28.1 occ:1.00 OD1 A:ASP264 2.1 21.7 1.0 OD1 A:ASP346 2.1 14.9 1.0 OAD A:SD4504 2.1 28.3 1.0 NE2 A:HIS94 2.2 12.4 1.0 OD2 A:ASP346 2.5 12.8 1.0 CG A:ASP346 2.6 15.2 1.0 ND2 A:SD4504 2.7 19.6 1.0 CG A:ASP264 2.9 20.2 1.0 CE1 A:HIS94 3.1 7.5 1.0 CD2 A:HIS94 3.3 14.3 1.0 OD2 A:ASP264 3.3 12.4 1.0 ZN A:ZN501 3.4 27.4 1.0 CG A:SD4504 3.6 22.9 1.0 OE1 A:GLU302 3.7 22.0 1.0 OE1 A:GLU301 3.9 22.5 1.0 CB A:ASN265 3.9 14.9 1.0 OD1 A:SD4504 4.0 23.8 1.0 N A:SD4504 4.1 34.6 1.0 CB A:ASP346 4.2 11.5 1.0 CG A:ASN265 4.2 15.3 1.0 ND1 A:HIS94 4.2 14.4 1.0 CB A:ASP264 4.2 16.7 1.0 CD A:GLU301 4.3 30.7 1.0 CG A:HIS94 4.4 13.9 1.0 OE2 A:GLU301 4.4 14.5 1.0 ND2 A:ASN265 4.4 10.5 1.0 CD A:GLU302 4.6 15.6 1.0 CA A:ASP264 4.7 15.4 1.0 OD1 A:ASN265 4.7 18.8 1.0 CB A:SD4504 4.7 29.0 1.0 O A:HOH607 4.7 13.6 1.0 N A:MET347 4.8 12.5 1.0 C A:ASP264 4.8 15.5 1.0 CA A:ASP346 4.9 15.0 1.0 CA A:ASN265 4.9 14.3 1.0 CA A:SD4504 4.9 36.2 1.0 N A:ASN265 4.9 15.8 1.0

A.Chaikuad, E.S.Pilka, A.D.Riso, F.V.Delft, K.L.Kavanagh, C.Venien-Bryan, U.Oppermann, W.W.Yue. Structure of Human Aspartyl Aminopeptidase Complexed with Substrate Analogue: Insight Into Catalytic Mechanism, Substrate Specificity and M18 Peptidase Family. Bmc Struct.Biol. V. 12 14 2012.
ISSN: ESSN 1472-6807
PubMed: 22720794
DOI: 10.1186/1472-6807-12-14