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Copper in PDB 5vg0: Room Temperature X-Ray Crystallographic Structure of A Jonesia Denitrificans Lytic Polysaccharide Monooxygenase at 1.1 Angstrom Resolution.

Enzymatic activity of Room Temperature X-Ray Crystallographic Structure of A Jonesia Denitrificans Lytic Polysaccharide Monooxygenase at 1.1 Angstrom Resolution.

All present enzymatic activity of Room Temperature X-Ray Crystallographic Structure of A Jonesia Denitrificans Lytic Polysaccharide Monooxygenase at 1.1 Angstrom Resolution.:
3.2.1.14;

Protein crystallography data

The structure of Room Temperature X-Ray Crystallographic Structure of A Jonesia Denitrificans Lytic Polysaccharide Monooxygenase at 1.1 Angstrom Resolution., PDB code: 5vg0 was solved by J.-P.Bacik, C.J.Unkefer, J.C.H.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.00 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.040, 75.560, 120.360, 90.00, 90.00, 90.00
R / Rfree (%) 11.4 / 12.8

Copper Binding Sites:

The binding sites of Copper atom in the Room Temperature X-Ray Crystallographic Structure of A Jonesia Denitrificans Lytic Polysaccharide Monooxygenase at 1.1 Angstrom Resolution. (pdb code 5vg0). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Room Temperature X-Ray Crystallographic Structure of A Jonesia Denitrificans Lytic Polysaccharide Monooxygenase at 1.1 Angstrom Resolution., PDB code: 5vg0:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 5vg0

Go back to Copper Binding Sites List in 5vg0
Copper binding site 1 out of 2 in the Room Temperature X-Ray Crystallographic Structure of A Jonesia Denitrificans Lytic Polysaccharide Monooxygenase at 1.1 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Room Temperature X-Ray Crystallographic Structure of A Jonesia Denitrificans Lytic Polysaccharide Monooxygenase at 1.1 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:11.4
occ:0.84
 O2 A:PER202 1.8 48.6 0.8
NE2 A:HIS109 2.0 14.2 1.0
ND1 A:HIS32 2.0 13.2 1.0
O1 A:PER202 2.1 48.6 0.8
N A:HIS32 2.2 11.1 1.0
O A:HOH301 2.5 29.3 1.0
HZ A:PHE164 2.8 15.1 1.0
CE1 A:HIS109 2.9 15.2 1.0
CG A:HIS32 3.0 12.2 1.0
CE1 A:HIS32 3.0 15.0 1.0
CD2 A:HIS109 3.0 13.0 1.0
HE1 A:HIS109 3.1 18.3 1.0
CA A:HIS32 3.1 9.9 1.0
HB3 A:ALA107 3.1 18.1 1.0
HB2 A:HIS32 3.2 13.8 1.0
HE1 A:HIS32 3.2 18.1 1.0
HD2 A:HIS109 3.2 15.6 1.0
CB A:HIS32 3.3 11.5 1.0
HA A:HIS32 3.4 11.9 1.0
CZ A:PHE164 3.5 12.6 1.0
CB A:ALA107 4.0 15.1 1.0
HE1 A:PHE164 4.0 14.8 1.0
ND1 A:HIS109 4.1 14.8 1.0
NE2 A:HIS32 4.1 16.2 1.0
CD2 A:HIS32 4.1 14.6 1.0
CE1 A:PHE164 4.1 12.3 1.0
HB1 A:ALA107 4.1 18.1 1.0
CG A:HIS109 4.1 12.8 1.0
HB3 A:HIS32 4.2 13.8 1.0
HE2 A:PHE164 4.3 14.4 1.0
CE2 A:PHE164 4.3 12.0 1.0
O A:HOH450 4.3 45.6 1.0
O A:HOH401 4.3 34.9 1.0
O A:ALA107 4.4 12.7 1.0
HB2 A:ALA107 4.4 18.1 1.0
C A:HIS32 4.5 9.0 1.0
O A:HIS32 4.8 9.8 1.0
DD1 A:HIS109 4.8 17.8 0.5
HD1 A:HIS109 4.8 17.8 0.5
HE2 A:HIS32 4.9 19.4 0.5
DE2 A:HIS32 4.9 19.4 0.5
HD2 A:HIS32 4.9 17.5 1.0
HH2 A:TRP155 5.0 13.8 1.0

Copper binding site 2 out of 2 in 5vg0

Go back to Copper Binding Sites List in 5vg0
Copper binding site 2 out of 2 in the Room Temperature X-Ray Crystallographic Structure of A Jonesia Denitrificans Lytic Polysaccharide Monooxygenase at 1.1 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Room Temperature X-Ray Crystallographic Structure of A Jonesia Denitrificans Lytic Polysaccharide Monooxygenase at 1.1 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:11.8
occ:0.89
 O2 B:PER202 1.8 31.0 0.9
ND1 B:HIS32 2.0 11.3 1.0
NE2 B:HIS109 2.0 16.5 1.0
N B:HIS32 2.1 11.2 1.0
O A:HOH307 2.3 30.6 1.0
HZ B:PHE164 2.5 15.8 1.0
O1 B:PER202 2.7 33.2 0.9
CE1 B:HIS109 2.9 19.2 1.0
CG B:HIS32 3.0 10.0 1.0
CE1 B:HIS32 3.0 12.5 1.0
CD2 B:HIS109 3.1 15.0 1.0
HE1 B:HIS109 3.1 23.1 1.0
CA B:HIS32 3.1 9.5 1.0
HB2 B:HIS32 3.2 11.9 1.0
CZ B:PHE164 3.2 13.2 1.0
HE1 B:HIS32 3.2 15.0 1.0
CB B:HIS32 3.2 9.9 1.0
HD2 B:HIS109 3.3 18.0 1.0
HA B:HIS32 3.3 11.4 1.0
HB3 B:ALA107 3.3 28.5 1.0
HE1 B:PHE164 3.9 15.1 1.0
HE2 B:PHE164 3.9 14.6 1.0
CE1 B:PHE164 3.9 12.6 1.0
CE2 B:PHE164 3.9 12.1 1.0
ND1 B:HIS109 4.1 19.4 1.0
O A:ASN159 4.1 14.6 1.0
NE2 B:HIS32 4.1 12.5 1.0
CD2 B:HIS32 4.1 11.2 1.0
CG B:HIS109 4.2 16.3 1.0
CB B:ALA107 4.2 23.7 1.0
HB3 B:HIS32 4.2 11.9 1.0
O B:ALA107 4.3 20.3 1.0
HB1 B:ALA107 4.3 28.5 1.0
C B:HIS32 4.5 9.5 1.0
HB2 B:ALA107 4.6 28.5 1.0
OE1 B:GLU65 4.7 18.6 0.5
OE1 B:GLU65 4.7 15.5 0.5
DD1 B:HIS109 4.8 23.2 0.5
HD1 B:HIS109 4.8 23.2 0.5
HA A:THR160 4.8 13.2 1.0
O B:HIS32 4.9 10.9 1.0
HE2 B:HIS32 4.9 14.9 0.5
DE2 B:HIS32 4.9 14.9 0.5
C A:ASN159 4.9 12.1 1.0
HD2 B:HIS32 5.0 13.4 1.0
HH2 B:TRP155 5.0 15.2 1.0

Reference:

J.P.Bacik, S.Mekasha, Z.Forsberg, A.Y.Kovalevsky, G.Vaaje-Kolstad, V.G.H.Eijsink, J.C.Nix, L.Coates, M.J.Cuneo, C.J.Unkefer, J.C.Chen. Neutron and Atomic Resolution X-Ray Structures of A Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence For N-Terminal Deprotonation. Biochemistry V. 56 2529 2017.
ISSN: ISSN 1520-4995
PubMed: 28481095
DOI: 10.1021/ACS.BIOCHEM.7B00019
Page generated: Mon Jul 14 05:29:05 2025

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