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

The structure of X-Ray Structure of Lpmo, PDB code: 6ydc 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 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.790, 120.800, 136.360, 90.00, 92.09, 90.00
R / Rfree (%)	21.5 / 26.2

The binding sites of Copper atom in the X-Ray Structure of Lpmo (pdb code 6ydc). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the X-Ray Structure of Lpmo, PDB code: 6ydc:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 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:13.5 occ:1.00 ND1 A:HIC1 2.0 13.4 1.0 NE2 A:HIS79 2.0 11.5 1.0 N A:HIC1 2.1 12.8 1.0 O A:HOH567 2.6 4.2 0.3 OH A:TYR169 2.6 8.9 1.0 CE1 A:HIC1 3.0 14.0 1.0 CG A:HIC1 3.0 13.3 1.0 CD2 A:HIS79 3.0 11.1 1.0 CE1 A:HIS79 3.1 10.9 1.0 CA A:HIC1 3.2 12.6 1.0 CB A:HIC1 3.4 12.9 1.0 CZ A:TYR169 3.6 8.9 1.0 C6 E:BGC1 3.7 44.9 1.0 OE1 A:GLN167 3.7 12.1 1.0 NE2 A:HIC1 4.1 14.2 1.0 CD2 A:HIC1 4.1 13.8 1.0 CG A:HIS79 4.1 10.9 1.0 O A:HOH426 4.2 14.0 1.0 ND1 A:HIS79 4.2 10.7 1.0 CE1 A:TYR169 4.3 9.0 1.0 O6 E:BGC1 4.3 41.1 1.0 O A:HOH557 4.3 6.8 0.7 CE2 A:TYR169 4.4 8.8 1.0 C A:HIC1 4.5 12.1 1.0 C5 E:BGC1 4.6 47.4 1.0 O5 E:BGC1 4.7 49.3 1.0 C4 E:BGC1 4.8 46.6 1.0 CD A:GLN167 4.8 11.7 1.0 CE1 A:HIS152 4.8 9.7 1.0 O A:HIC1 5.0 12.3 1.0

Copper binding site 2 out of 4 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:9.9 occ:1.00 ND1 B:HIC1 1.9 9.8 1.0 NE2 B:HIS79 2.0 9.8 1.0 N B:HIC1 2.1 9.3 1.0 O B:HOH593 2.6 4.6 0.3 OH B:TYR169 2.7 9.0 1.0 CE1 B:HIC1 2.9 9.7 1.0 CG B:HIC1 2.9 9.7 1.0 CD2 B:HIS79 3.0 9.5 1.0 CE1 B:HIS79 3.0 9.6 1.0 CA B:HIC1 3.2 9.1 1.0 CB B:HIC1 3.3 9.3 1.0 CZ B:TYR169 3.7 9.0 1.0 OE1 B:GLN167 3.8 9.6 1.0 C6 F:BGC1 3.8 37.8 0.7 O B:HOH466 4.0 15.2 1.0 NE2 B:HIC1 4.0 9.9 1.0 CD2 B:HIC1 4.0 9.8 1.0 ND1 B:HIS79 4.1 9.7 1.0 CG B:HIS79 4.1 9.5 1.0 O6 F:BGC1 4.2 36.0 0.7 O5 F:BGC1 4.2 44.3 0.7 O B:HOH604 4.3 12.3 0.7 CE1 B:TYR169 4.4 9.0 1.0 C5 F:BGC1 4.4 40.4 0.7 C B:HIC1 4.5 8.7 1.0 CE2 B:TYR169 4.6 8.7 1.0 C4 F:BGC1 4.6 42.0 0.7 CE1 B:HIS152 4.8 8.0 1.0 CD B:GLN167 4.9 8.8 1.0 O B:HIC1 4.9 8.4 1.0 NE2 B:HIS152 5.0 8.1 1.0

Copper binding site 3 out of 4 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 3 of X-Ray Structure of Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu301 b:12.4 occ:1.00 ND1 C:HIC1 2.0 12.6 1.0 NE2 C:HIS79 2.0 11.0 1.0 N C:HIC1 2.1 11.2 1.0 OH C:TYR169 2.7 9.9 1.0 O C:HOH560 2.7 6.2 0.3 CG C:HIC1 2.9 12.3 1.0 CE1 C:HIC1 2.9 13.1 1.0 CD2 C:HIS79 2.9 10.5 1.0 O C:HOH540 3.1 36.0 1.0 CE1 C:HIS79 3.1 10.6 1.0 CA C:HIC1 3.2 10.9 1.0 CB C:HIC1 3.3 11.4 1.0 CZ C:TYR169 3.7 9.3 1.0 OE1 C:GLN167 3.8 9.9 1.0 O C:HOH511 3.9 19.9 1.0 NE2 C:HIC1 4.0 13.6 1.0 CD2 C:HIC1 4.1 12.9 1.0 CG C:HIS79 4.1 10.5 1.0 ND1 C:HIS79 4.1 10.5 1.0 CE2 C:TYR169 4.3 9.2 1.0 C C:HIC1 4.5 10.4 1.0 O C:HOH550 4.5 22.2 0.7 CE1 C:TYR169 4.6 9.0 1.0 O C:HOH609 4.6 33.5 1.0 CE1 C:HIS152 4.9 10.7 1.0 CD C:GLN167 4.9 8.9 1.0 O C:HIC1 4.9 10.4 1.0

Copper binding site 4 out of 4 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 4 of X-Ray Structure of Lpmo within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu301 b:8.5 occ:1.00 ND1 D:HIC1 2.0 9.2 1.0 NE2 D:HIS79 2.1 8.2 1.0 N D:HIC1 2.1 8.1 1.0 O D:HOH550 2.6 6.7 0.3 OH D:TYR169 2.7 7.7 1.0 CG D:HIC1 2.9 9.2 1.0 CE1 D:HIC1 2.9 9.3 1.0 CD2 D:HIS79 3.0 7.8 1.0 CE1 D:HIS79 3.1 7.9 1.0 CA D:HIC1 3.2 8.5 1.0 CB D:HIC1 3.3 8.5 1.0 O D:HOH628 3.5 32.6 1.0 CZ D:TYR169 3.7 7.7 1.0 OE1 D:GLN167 3.7 8.2 1.0 O D:HOH463 3.9 15.3 1.0 NE2 D:HIC1 4.1 9.4 1.0 CD2 D:HIC1 4.1 9.4 1.0 CG D:HIS79 4.1 7.9 1.0 ND1 D:HIS79 4.2 8.0 1.0 CE2 D:TYR169 4.3 7.6 1.0 C D:HIC1 4.5 8.5 1.0 CE1 D:TYR169 4.5 8.0 1.0 O D:HOH572 4.7 17.5 0.7 CD D:GLN167 4.8 8.2 1.0 O D:HIC1 4.9 8.6 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