Copper in PDB 5yfd: 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: 5yfd was solved by T.Xu, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.99 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.460, 207.140, 58.990, 90.00, 90.02, 90.00
R / Rfree (%)	18 / 21.7

The binding sites of Copper atom in the Crystal Structure of A New Dpp III Family Member (pdb code 5yfd). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of A New Dpp III Family Member, PDB code: 5yfd:
Jump to Copper binding site number: 1; 2;

Copper 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 Copper with other atoms in the Cu 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:Cu806 b:15.5 occ:0.50 NE2 A:HIS448 1.9 7.6 1.0 OE2 A:GLU501 2.0 6.6 1.0 NE2 A:HIS443 2.2 16.0 1.0 O A:HOH1231 2.2 21.4 1.0 CE1 A:HIS448 2.8 8.1 1.0 CD A:GLU501 2.8 6.7 1.0 CD2 A:HIS448 2.9 7.8 1.0 OE1 A:GLU501 3.0 10.3 1.0 CE1 A:HIS443 3.1 15.8 1.0 CD2 A:HIS443 3.2 14.1 1.0 O A:HOH1210 3.8 11.7 1.0 ND1 A:HIS448 4.0 7.4 1.0 CG A:HIS448 4.1 6.9 1.0 O A:HOH1187 4.1 11.5 1.0 NE2 A:HIS562 4.2 6.3 1.0 ND1 A:HIS443 4.2 14.4 1.0 CG A:GLU501 4.3 5.9 1.0 CG A:HIS443 4.3 11.9 1.0 OE2 A:GLU444 4.4 8.8 1.0 OE1 A:GLU444 4.4 11.7 1.0 OH A:TYR313 4.5 14.0 1.0 CB A:ALA504 4.5 5.3 1.0 CD2 A:HIS562 4.7 6.5 1.0 CA A:GLU501 4.8 4.9 1.0 CD A:GLU444 4.8 9.0 1.0 CB A:GLU501 4.9 5.3 1.0

Copper 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 Copper with other atoms in the Cu 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:Cu806 b:16.7 occ:0.50 NE2 B:HIS448 1.9 8.8 1.0 OE2 B:GLU501 2.0 6.5 1.0 NE2 B:HIS443 2.2 14.6 1.0 O B:HOH1217 2.4 16.4 1.0 CE1 B:HIS448 2.8 8.8 1.0 CD B:GLU501 2.8 6.5 1.0 CD2 B:HIS448 2.9 8.7 1.0 OE1 B:GLU501 2.9 8.7 1.0 CE1 B:HIS443 3.1 14.0 1.0 CD2 B:HIS443 3.2 13.7 1.0 O B:HOH1154 3.8 11.9 1.0 ND1 B:HIS448 3.9 8.5 1.0 CG B:HIS448 4.0 7.8 1.0 ND1 B:HIS443 4.2 13.3 1.0 NE2 B:HIS562 4.3 6.1 1.0 CG B:GLU501 4.3 6.0 1.0 CG B:HIS443 4.3 12.0 1.0 OE2 B:GLU444 4.3 7.8 1.0 OE1 B:GLU444 4.4 11.2 1.0 OH B:TYR313 4.5 15.0 1.0 CB B:ALA504 4.6 5.3 1.0 CD2 B:HIS562 4.7 5.9 1.0 CD B:GLU444 4.7 8.7 1.0 CA B:GLU501 4.8 5.0 1.0 CB B:GLU501 4.9 5.3 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