Copper in PDB 5nlt: CVAA9A

The structure of CVAA9A, PDB code: 5nlt was solved by K.E.H.Frandsen, J.-C.N.Poulsen, T.Tandrup, K.Schnorr, M.Tovborg, L.Loleggio, 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 1
Cell size a, b, c (Å), α, β, γ (°)	47.000, 59.420, 115.450, 102.67, 98.89, 89.54
R / Rfree (%)	19.8 / 24.4

The binding sites of Copper atom in the CVAA9A (pdb code 5nlt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the CVAA9A, PDB code: 5nlt:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in the CVAA9A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of CVAA9A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu301 b:21.8 occ:1.00 ND1 A:HIC1 2.0 26.4 1.0 NE2 A:HIS79 2.0 17.6 1.0 N A:HIC1 2.0 21.2 1.0 OH A:TYR169 2.7 16.5 1.0 CD2 A:HIS79 2.9 16.1 1.0 CE1 A:HIC1 3.0 28.0 1.0 CG A:HIC1 3.0 23.3 1.0 CE1 A:HIS79 3.0 16.4 1.0 CA A:HIC1 3.1 21.0 1.0 O A:HOH538 3.4 33.6 1.0 CB A:HIC1 3.4 22.4 1.0 OE1 A:GLN167 3.7 17.5 1.0 CZ A:TYR169 3.7 15.6 1.0 O A:HOH427 3.9 16.6 1.0 CG A:HIS79 4.0 15.9 1.0 ND1 A:HIS79 4.1 15.6 1.0 NE2 A:HIC1 4.1 29.8 1.0 CD2 A:HIC1 4.1 26.0 1.0 CE1 A:TYR169 4.4 14.9 1.0 C A:HIC1 4.4 19.2 1.0 CE2 A:TYR169 4.6 15.7 1.0 O A:HOH513 4.6 22.3 1.0 CD A:GLN167 4.9 17.2 1.0 O A:HIC1 4.9 18.6 1.0

Copper binding site 2 out of 6 in the CVAA9A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of CVAA9A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu301 b:28.6 occ:1.00 ND1 B:HIC1 2.0 29.0 1.0 NE2 B:HIS79 2.1 25.6 1.0 N B:HIC1 2.1 28.5 1.0 OH B:TYR169 2.6 21.2 1.0 CE1 B:HIC1 2.9 28.2 1.0 CD2 B:HIS79 2.9 24.1 1.0 CG B:HIC1 3.0 28.0 1.0 O B:HOH579 3.1 36.0 1.0 CE1 B:HIS79 3.1 24.0 1.0 CA B:HIC1 3.2 26.3 1.0 CB B:HIC1 3.4 27.8 1.0 OE1 B:GLN167 3.6 22.4 1.0 CZ B:TYR169 3.7 21.5 1.0 O B:HOH465 3.8 17.7 1.0 NE2 B:HIC1 4.1 27.6 1.0 CD2 B:HIC1 4.1 26.9 1.0 CG B:HIS79 4.1 23.6 1.0 ND1 B:HIS79 4.2 23.3 1.0 CE2 B:TYR169 4.3 19.7 1.0 C B:HIC1 4.5 24.3 1.0 CE1 B:TYR169 4.6 20.2 1.0 CD B:GLN167 4.8 22.7 1.0 O B:HIC1 5.0 24.6 1.0 CE1 B:HIS152 5.0 25.7 1.0

Copper binding site 3 out of 6 in the CVAA9A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of CVAA9A within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu301 b:38.9 occ:1.00 ND1 C:HIC1 2.0 46.0 1.0 NE2 C:HIS79 2.0 33.4 1.0 N C:HIC1 2.1 40.4 1.0 OH C:TYR169 2.6 25.0 1.0 CD2 C:HIS79 2.9 29.5 1.0 CE1 C:HIC1 3.0 48.3 1.0 CG C:HIC1 3.0 45.6 1.0 CE1 C:HIS79 3.1 29.6 1.0 CA C:HIC1 3.2 38.7 1.0 CB C:HIC1 3.5 42.7 1.0 OE1 C:GLN167 3.6 26.2 1.0 CZ C:TYR169 3.6 23.6 1.0 O C:HOH509 3.9 26.9 1.0 CG C:HIS79 4.1 27.3 1.0 NE2 C:HIC1 4.1 46.8 1.0 ND1 C:HIS79 4.1 27.7 1.0 CD2 C:HIC1 4.2 45.7 1.0 CE2 C:TYR169 4.3 23.6 1.0 C C:HIC1 4.5 38.4 1.0 CE1 C:TYR169 4.6 22.8 1.0 O C:HOH558 4.6 44.4 1.0 CD C:GLN167 4.8 23.4 1.0 O C:HOH537 4.8 38.0 1.0 CE1 C:HIS152 5.0 22.0 1.0

Copper binding site 4 out of 6 in the CVAA9A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of CVAA9A within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu301 b:27.9 occ:1.00 N D:HIC1 2.0 29.0 1.0 ND1 D:HIC1 2.0 30.5 1.0 NE2 D:HIS79 2.0 25.0 1.0 OH D:TYR169 2.7 20.4 1.0 CD2 D:HIS79 2.9 22.7 1.0 CG D:HIC1 3.0 28.4 1.0 CE1 D:HIC1 3.0 31.0 1.0 CE1 D:HIS79 3.1 22.5 1.0 CA D:HIC1 3.1 27.1 1.0 CB D:HIC1 3.4 28.3 1.0 OE1 D:GLN167 3.7 19.1 1.0 CZ D:TYR169 3.7 19.8 1.0 O4 D:SO4302 3.9 44.6 1.0 O D:HOH407 3.9 15.8 1.0 CG D:HIS79 4.0 20.4 1.0 ND1 D:HIS79 4.1 22.8 1.0 NE2 D:HIC1 4.1 33.1 1.0 CD2 D:HIC1 4.2 30.4 1.0 CE1 D:TYR169 4.4 19.6 1.0 C D:HIC1 4.4 26.2 1.0 CE2 D:TYR169 4.5 19.1 1.0 O3 D:SO4302 4.5 53.1 1.0 S D:SO4302 4.6 62.6 1.0 O D:HOH462 4.6 34.4 1.0 O2 D:SO4302 4.6 54.6 1.0 CD D:GLN167 4.8 20.1 1.0 O D:HIC1 4.9 25.9 1.0

Copper binding site 5 out of 6 in the CVAA9A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of CVAA9A within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu301 b:27.9 occ:1.00 ND1 E:HIC1 1.9 34.8 1.0 NE2 E:HIS79 2.1 26.5 1.0 N E:HIC1 2.1 30.4 1.0 OH E:TYR169 2.6 24.0 1.0 CE1 E:HIC1 2.9 39.0 1.0 CG E:HIC1 2.9 33.0 1.0 CD2 E:HIS79 2.9 24.1 1.0 CE1 E:HIS79 3.1 23.8 1.0 O4 E:SO4302 3.1 62.6 1.0 CA E:HIC1 3.2 28.4 1.0 O E:HOH496 3.2 36.9 1.0 CB E:HIC1 3.4 31.3 1.0 OE1 E:GLN167 3.6 23.6 1.0 CZ E:TYR169 3.7 21.0 1.0 NE2 E:HIC1 4.0 38.3 1.0 CD2 E:HIC1 4.1 34.9 1.0 O E:HOH446 4.1 24.9 1.0 CG E:HIS79 4.1 25.1 1.0 ND1 E:HIS79 4.2 23.5 1.0 CE2 E:TYR169 4.3 20.2 1.0 S E:SO4302 4.4 64.3 1.0 C E:HIC1 4.5 25.0 1.0 O3 E:SO4302 4.6 55.1 1.0 CE1 E:TYR169 4.6 20.8 1.0 CD E:GLN167 4.8 22.0 1.0

Copper binding site 6 out of 6 in the CVAA9A


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of CVAA9A within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu301 b:37.1 occ:1.00 ND1 F:HIC1 2.0 42.6 1.0 NE2 F:HIS79 2.0 33.2 1.0 N F:HIC1 2.0 38.4 1.0 OH F:TYR169 2.8 30.0 1.0 CD2 F:HIS79 2.9 32.1 1.0 CE1 F:HIC1 2.9 47.5 1.0 CG F:HIC1 3.0 41.6 1.0 CE1 F:HIS79 3.0 30.0 1.0 CA F:HIC1 3.1 36.4 1.0 O F:HOH541 3.2 13.0 0.5 O3 F:SO4303 3.2 93.3 1.0 CB F:HIC1 3.4 38.7 1.0 OE1 F:GLN167 3.7 39.0 1.0 CZ F:TYR169 3.8 30.9 1.0 CG F:HIS79 4.1 33.0 1.0 NE2 F:HIC1 4.1 52.0 1.0 ND1 F:HIS79 4.1 34.3 1.0 CD2 F:HIC1 4.1 44.0 1.0 O F:HOH430 4.2 34.3 1.0 C F:HIC1 4.5 33.9 1.0 CE1 F:TYR169 4.5 30.4 1.0 S F:SO4303 4.6 0.7 1.0 CE2 F:TYR169 4.7 29.3 1.0 O F:HOH541 4.8 16.4 0.5 CD F:GLN167 4.9 36.6 1.0 O F:HIC1 4.9 33.9 1.0

T.J.Simmons, K.E.H.Frandsen, L.Ciano, T.Tryfona, N.Lenfant, J.C.Poulsen, L.F.L.Wilson, T.Tandrup, M.Tovborg, K.Schnorr, K.S.Johansen, B.Henrissat, P.H.Walton, L.Lo Leggio, P.Dupree. Structural and Electronic Determinants of Lytic Polysaccharide Monooxygenase Reactivity on Polysaccharide Substrates. Nat Commun V. 8 1064 2017.
ISSN: ESSN 2041-1723
PubMed: 29057953
DOI: 10.1038/S41467-017-01247-3