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

The structure of X-Ray Structure of Lpmo, PDB code: 6ydd 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)	2.87 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.140, 39.700, 120.650, 90.00, 93.49, 90.00
R / Rfree (%)	19.8 / 26.1

The binding sites of Copper atom in the X-Ray Structure of Lpmo (pdb code 6ydd). 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: 6ydd:
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:20.1 occ:1.00 ND1 A:HIC306 2.0 18.4 1.0 N A:HIC306 2.1 17.0 1.0 NE2 A:HIS79 2.1 16.0 1.0 OH A:TYR169 2.8 8.9 1.0 CG A:HIC306 2.9 17.5 1.0 CE1 A:HIC306 3.0 18.3 1.0 CD2 A:HIS79 3.0 14.8 1.0 CE1 A:HIS79 3.2 15.0 1.0 CA A:HIC306 3.2 16.2 1.0 CB A:HIC306 3.4 16.8 1.0 C6 C:BGC1 3.7 46.6 1.0 CZ A:TYR169 3.8 9.2 1.0 O A:HOH403 3.9 31.9 1.0 OE1 A:GLN167 4.0 11.6 1.0 NE2 A:HIC306 4.1 18.3 1.0 CD2 A:HIC306 4.1 17.9 1.0 CG A:HIS79 4.2 14.3 1.0 ND1 A:HIS79 4.2 14.5 1.0 CE1 A:TYR169 4.3 9.2 1.0 O6 C:BGC1 4.4 47.9 1.0 C4 C:BGC1 4.4 43.7 1.0 C5 C:BGC1 4.5 46.0 1.0 C A:HIC306 4.5 15.1 1.0 O5 C:BGC1 4.6 46.8 1.0 CE2 A:TYR169 4.7 9.2 1.0 CE1 A:HIS152 4.9 12.2 1.0 O A:HIC306 4.9 15.1 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:20.0 occ:1.00 ND1 B:HIC304 2.0 17.4 1.0 N B:HIC304 2.1 16.4 1.0 NE2 B:HIS79 2.1 17.7 1.0 OH B:TYR169 2.7 10.5 1.0 CD2 B:HIS79 2.9 16.7 1.0 CG B:HIC304 3.0 16.5 1.0 CE1 B:HIC304 3.0 16.9 1.0 CE1 B:HIS79 3.2 17.1 1.0 O B:HOH412 3.2 28.3 1.0 CA B:HIC304 3.3 15.3 1.0 CB B:HIC304 3.5 15.9 1.0 O B:HOH415 3.7 29.2 1.0 CZ B:TYR169 3.7 10.5 1.0 OE1 B:GLN167 3.9 10.0 1.0 NE2 B:HIC304 4.1 16.9 1.0 CD2 B:HIC304 4.1 16.8 1.0 CG B:HIS79 4.1 16.0 1.0 ND1 B:HIS79 4.2 16.4 1.0 CE2 B:TYR169 4.3 10.6 1.0 C B:HIC304 4.6 13.9 1.0 CE1 B:TYR169 4.7 10.4 1.0 CE1 B:HIS152 4.9 14.7 1.0 O B:HIC304 4.9 13.7 1.0 O2 D:BGC1 4.9 34.4 1.0 O1 D:BGC1 5.0 32.4 1.0 O B:HOH414 5.0 43.9 1.0 C1 D:BGC1 5.0 34.1 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