Zinc in PDB 3var: Crystal Structure of Dnpep, Znzn Form

All present enzymatic activity of Crystal Structure of Dnpep, Znzn Form:
3.4.11.21;

The structure of Crystal Structure of Dnpep, Znzn Form, PDB code: 3var was solved by P.D.Kiser, Y.Chen, K.Palczewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.68 / 2.25
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	245.162, 245.162, 245.162, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.8

The binding sites of Zinc atom in the Crystal Structure of Dnpep, Znzn Form (pdb code 3var). 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 Dnpep, Znzn Form, PDB code: 3var:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Dnpep, Znzn Form


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 Dnpep, Znzn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:25.4 occ:1.00 OD1 A:ASP367 2.1 16.2 1.0 OD1 A:ASP285 2.1 16.1 1.0 NE2 A:HIS115 2.2 14.0 1.0 O A:HOH773 2.5 31.7 1.0 OD2 A:ASP367 2.5 16.3 1.0 CG A:ASP367 2.6 17.2 1.0 CG A:ASP285 3.0 15.7 1.0 CE1 A:HIS115 3.2 14.2 1.0 CD2 A:HIS115 3.2 13.9 1.0 OD2 A:ASP285 3.3 14.4 1.0 ZN A:ZN502 3.3 29.6 1.0 OE2 A:GLU323 3.8 22.5 1.0 CB A:ASN286 3.9 16.1 1.0 OE1 A:GLU322 3.9 22.7 1.0 CB A:ASP367 4.2 17.8 1.0 CG A:ASN286 4.2 17.0 1.0 ND1 A:HIS115 4.3 14.4 1.0 CG A:HIS115 4.4 14.4 1.0 CB A:ASP285 4.4 16.2 1.0 CD A:GLU322 4.4 22.6 1.0 ND2 A:ASN286 4.5 14.9 1.0 N A:MET368 4.7 23.2 1.0 CD A:GLU323 4.7 19.5 1.0 OE2 A:GLU322 4.7 25.9 1.0 OD1 A:ASN286 4.8 18.0 1.0 CA A:ASP367 4.8 18.8 1.0 O A:HOH771 4.8 25.7 1.0 CA A:ASP285 4.8 16.5 1.0 C A:ASP285 4.9 16.1 1.0 CA A:ASN286 4.9 16.5 1.0 N A:ASN286 5.0 16.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Dnpep, Znzn Form


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 Dnpep, Znzn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:29.6 occ:1.00 OE2 A:GLU323 2.0 22.5 1.0 OD2 A:ASP285 2.1 14.4 1.0 NE2 A:HIS461 2.2 23.1 1.0 O A:HOH773 2.3 31.7 1.0 OE1 A:GLU323 2.7 19.9 1.0 CD A:GLU323 2.7 19.5 1.0 CG A:ASP285 3.1 15.7 1.0 CD2 A:HIS461 3.1 21.7 1.0 CE1 A:HIS461 3.2 21.2 1.0 ZN A:ZN501 3.3 25.4 1.0 OD1 A:ASP285 3.5 16.1 1.0 CG A:GLU323 4.2 20.0 1.0 OE1 A:GLU322 4.3 22.7 1.0 ND1 A:HIS461 4.3 21.5 1.0 CG A:HIS461 4.4 20.6 1.0 CB A:ASP285 4.4 16.2 1.0 NE2 A:HIS115 4.5 14.0 1.0 CE1 A:HIS115 4.5 14.2 1.0 CD A:PRO119 4.7 16.6 1.0 CG A:MET460 4.8 29.4 1.0 SD A:MET460 4.8 34.6 1.0 CG A:PRO119 4.8 17.3 1.0 O A:HOH664 5.0 17.5 1.0

Y.Chen, E.R.Farquhar, M.R.Chance, K.Palczewski, P.D.Kiser. Insights Into Substrate Specificity and Metal Activation of Mammalian Tetrahedral Aspartyl Aminopeptidase. J.Biol.Chem. V. 287 13356 2012.
ISSN: ISSN 0021-9258
PubMed: 22356908
DOI: 10.1074/JBC.M112.347518