Zinc in PDB 5yfb: Crystal Structure of A New Dpp III Family Member

All present enzymatic activity of Crystal Structure of A New Dpp III Family Member:
3.4.14.4;

The structure of Crystal Structure of A New Dpp III Family Member, PDB code: 5yfb was solved by T.Xu, Z.Sun, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	98.27 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	207.208, 84.630, 90.220, 90.00, 108.46, 90.00
R / Rfree (%)	18.7 / 24.8

The binding sites of Zinc atom in the Crystal Structure of A New Dpp III Family Member (pdb code 5yfb). 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 A New Dpp III Family Member, PDB code: 5yfb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A New Dpp III Family Member


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 A New Dpp III Family Member within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:15.4 occ:1.00 NE2 A:HIS448 1.9 10.4 1.0 OE2 A:GLU501 2.0 13.6 1.0 O A:HOH1015 2.0 11.6 1.0 NE2 A:HIS443 2.0 16.3 1.0 O A:HOH1029 2.5 20.1 1.0 CD A:GLU501 2.7 15.6 1.0 OE1 A:GLU501 2.7 15.8 1.0 CE1 A:HIS448 2.8 11.9 1.0 CE1 A:HIS443 3.0 16.3 1.0 CD2 A:HIS443 3.1 15.7 1.0 CD2 A:HIS448 3.1 10.7 1.0 ND1 A:HIS448 4.0 11.4 1.0 NE2 A:HIS562 4.0 16.1 1.0 ND1 A:HIS443 4.1 15.6 1.0 CG A:HIS448 4.1 11.6 1.0 CG A:GLU501 4.1 15.1 1.0 CG A:HIS443 4.2 16.3 1.0 OH A:TYR313 4.3 19.6 1.0 C3 A:GOL804 4.3 30.2 1.0 O3 A:GOL804 4.3 23.2 1.0 CD2 A:HIS562 4.5 15.0 1.0 CB A:ALA504 4.5 15.8 1.0 OE2 A:GLU444 4.6 12.7 1.0 CA A:GLU501 4.7 14.9 1.0 CB A:GLU501 4.8 15.4 1.0 OE1 A:GLU444 4.8 13.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A New Dpp III Family Member


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 A New Dpp III Family Member within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:23.9 occ:1.00 NE2 B:HIS448 1.9 19.0 1.0 OE2 B:GLU501 2.0 25.5 1.0 NE2 B:HIS443 2.0 26.2 1.0 O B:HOH1025 2.3 22.0 1.0 CD B:GLU501 2.7 25.1 1.0 OE1 B:GLU501 2.8 27.1 1.0 CD2 B:HIS448 2.8 21.7 1.0 CE1 B:HIS443 2.9 26.4 1.0 CE1 B:HIS448 2.9 22.3 1.0 CD2 B:HIS443 3.1 24.7 1.0 CG B:HIS448 4.0 21.7 1.0 ND1 B:HIS448 4.0 21.0 1.0 ND1 B:HIS443 4.1 26.8 1.0 NE2 B:HIS562 4.1 25.6 1.0 CG B:HIS443 4.2 23.9 1.0 CG B:GLU501 4.2 24.8 1.0 CD2 B:HIS562 4.4 25.5 1.0 OH B:TYR313 4.5 23.3 1.0 CB B:ALA504 4.6 19.6 1.0 OE2 B:GLU444 4.6 21.6 1.0 CB B:GLU501 4.7 23.7 1.0 CA B:GLU501 4.8 23.1 1.0 OE1 B:GLU444 4.8 23.1 1.0

T.Xu, C.Xie, D.Yao, C.Z.Zhou, J.Liu. Crystal Structures of Aflatoxin-Oxidase From Armillariella Tabescens Reveal A Dual Activity Enzyme. Biochem. Biophys. Res. V. 494 621 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 29050944
DOI: 10.1016/J.BBRC.2017.10.077