Copper in PDB 6ydf: X-Ray Structure of Lpmo

The structure of X-Ray Structure of Lpmo, PDB code: 6ydf was solved by T.Tandrup, T.Tryfona, K.E.H.Frandsen, K.S.Johansen, P.Dupree, L.Lo Leggio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.12
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.120, 39.390, 119.930, 90.00, 93.78, 90.00
R / Rfree (%)	19.7 / 24.9

The binding sites of Copper atom in the X-Ray Structure of Lpmo (pdb code 6ydf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the X-Ray Structure of Lpmo, PDB code: 6ydf:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the X-Ray Structure of Lpmo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Structure of Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu301 b:14.7 occ:0.75 ND1 A:HIC302 2.0 18.5 1.0 N A:HIC302 2.0 17.8 1.0 NE2 A:HIS79 2.1 15.1 1.0 OH A:TYR169 2.7 13.5 1.0 CE1 A:HIC302 2.9 19.3 1.0 CD2 A:HIS79 3.0 15.4 1.0 O A:HOH498 3.0 49.6 1.0 CG A:HIC302 3.0 19.0 1.0 CE1 A:HIS79 3.2 15.3 1.0 CA A:HIC302 3.3 17.8 1.0 CB A:HIC302 3.5 17.8 1.0 OE1 A:GLN167 3.6 16.4 1.0 CZ A:TYR169 3.7 12.8 1.0 O1 A:SO4303 3.7 85.0 1.0 O A:HOH457 4.0 28.5 1.0 NE2 A:HIC302 4.1 19.0 1.0 CD2 A:HIC302 4.2 18.5 1.0 CG A:HIS79 4.2 15.5 1.0 ND1 A:HIS79 4.2 15.4 1.0 CE1 A:TYR169 4.3 12.4 1.0 CE2 A:TYR169 4.6 12.6 1.0 C A:HIC302 4.6 17.6 1.0 CD A:GLN167 4.7 15.2 1.0 S A:SO4303 5.0 86.4 1.0

Copper binding site 2 out of 2 in the X-Ray Structure of Lpmo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Structure of Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu301 b:19.5 occ:0.75 ND1 B:HIC302 2.0 21.2 1.0 N B:HIC302 2.0 20.4 1.0 NE2 B:HIS79 2.1 16.3 1.0 OH B:TYR169 2.6 16.1 1.0 CD2 B:HIS79 2.8 15.3 1.0 CE1 B:HIC302 3.0 22.2 1.0 CG B:HIC302 3.0 21.2 1.0 O B:HOH458 3.1 53.1 1.0 CE1 B:HIS79 3.2 15.1 1.0 CA B:HIC302 3.3 20.4 1.0 CB B:HIC302 3.5 20.7 1.0 CZ B:TYR169 3.6 15.7 1.0 OE1 B:GLN167 3.6 17.5 1.0 O B:HOH464 3.8 55.6 1.0 O B:HOH427 4.0 41.7 1.0 CG B:HIS79 4.1 14.9 1.0 NE2 B:HIC302 4.1 22.9 1.0 CE2 B:TYR169 4.2 15.6 1.0 CD2 B:HIC302 4.2 22.0 1.0 ND1 B:HIS79 4.2 15.0 1.0 CE1 B:TYR169 4.5 15.4 1.0 C B:HIC302 4.5 19.6 1.0 CD B:GLN167 4.7 17.4 1.0 O B:HIC302 4.9 21.6 1.0

T.Tandrup, T.Tryfona, K.E.H.Frandsen, K.S.Johansen, P.Dupree, L.Lo Leggio. Oligosaccharide Binding and Thermostability of Two Related AA9 Lytic Polysaccharide Monooxygenases. Biochemistry V. 59 3347 2020.
ISSN: ISSN 0006-2960
PubMed: 32818374
DOI: 10.1021/ACS.BIOCHEM.0C00312