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

The structure of X-Ray Structure of Lpmo, PDB code: 6ydg 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 / 1.90
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	125.670, 125.670, 125.670, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 26.1

The structure of X-Ray Structure of Lpmo also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Copper atom in the X-Ray Structure of Lpmo (pdb code 6ydg). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total only one binding site of Copper was determined in the X-Ray Structure of Lpmo, PDB code: 6ydg:

Copper binding site 1 out of 1 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:26.5 occ:1.00 O A:HOH401 1.8 16.9 0.5 ND1 A:HIC1 2.0 25.6 1.0 NE2 A:HIS78 2.0 29.9 1.0 N A:HIC1 2.1 26.0 1.0 OH A:TYR164 2.7 13.9 1.0 CG A:HIC1 2.8 27.3 1.0 CD2 A:HIS78 2.9 27.8 1.0 CE1 A:HIC1 3.0 26.0 1.0 CE1 A:HIS78 3.1 30.2 1.0 CA A:HIC1 3.2 25.9 1.0 CB A:HIC1 3.2 25.5 1.0 CZ A:TYR164 3.7 19.1 1.0 C6 B:BGC2 3.9 43.1 1.0 OE1 A:GLN162 3.9 27.8 1.0 CL A:CL307 4.0 48.1 1.0 CD2 A:HIC1 4.0 26.9 1.0 NE2 A:HIC1 4.1 25.2 1.0 CG A:HIS78 4.1 27.4 1.0 ND1 A:HIS78 4.1 28.2 1.0 O A:HOH438 4.1 35.4 1.0 O6 B:BGC2 4.3 41.1 1.0 CE1 A:TYR164 4.3 20.2 1.0 CE2 A:TYR164 4.4 20.6 1.0 O5 B:BGC2 4.5 48.3 1.0 C A:HIC1 4.5 25.4 1.0 C5 B:BGC2 4.6 42.1 1.0 C4 B:BGC2 4.7 39.9 1.0 NE2 A:HIS147 4.8 28.8 1.0 CD A:GLN162 5.0 28.1 1.0 O A:HIC1 5.0 29.9 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