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Copper in PDB 5nlt: CVAA9A

Protein crystallography data

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

Copper Binding Sites:

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 5nlt

Go back to Copper Binding Sites List in 5nlt
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 5nlt

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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 5nlt

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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 5nlt

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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 5nlt

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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 5nlt

Go back to Copper Binding Sites List in 5nlt
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

Reference:

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
Page generated: Sun Dec 13 11:19:03 2020

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