Copper in PDB 7zn6: Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus
Enzymatic activity of Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus
All present enzymatic activity of Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus:
1.10.3.2;
Protein crystallography data
The structure of Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus, PDB code: 7zn6
was solved by
C.Kosinas,
M.Dimarogona,
A.Zerva,
E.Topakas,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
74.97 /
1.90
|
|
Space group
|
P 43
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.855,
74.855,
118.948,
90,
90,
90
|
|
R / Rfree (%)
|
15.2 /
18.5
|
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus
(pdb code 7zn6). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the
Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus, PDB code: 7zn6:
Jump to Copper binding site number:
1;
2;
3;
4;
Copper binding site 1 out
of 4 in 7zn6
Go back to
Copper Binding Sites List in 7zn6
Copper binding site 1 out
of 4 in the Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu710
b:28.5
occ:1.00
|
HE2
|
A:HIS488
|
1.2
|
30.0
|
0.0
|
|
HE2
|
A:HIS117
|
1.2
|
30.0
|
0.0
|
|
HE2
|
A:HIS558
|
1.4
|
30.0
|
0.0
|
|
NE2
|
A:HIS488
|
2.0
|
23.8
|
1.0
|
|
NE2
|
A:HIS558
|
2.1
|
24.7
|
1.0
|
|
NE2
|
A:HIS117
|
2.1
|
28.1
|
1.0
|
|
O1
|
A:OXY707
|
2.5
|
32.0
|
1.0
|
|
O2
|
A:OXY707
|
2.5
|
38.1
|
1.0
|
|
CE1
|
A:HIS488
|
2.7
|
24.1
|
1.0
|
|
HE1
|
A:HIS488
|
2.7
|
24.4
|
1.0
|
|
CD2
|
A:HIS558
|
3.0
|
25.0
|
1.0
|
|
CD2
|
A:HIS117
|
3.0
|
25.6
|
1.0
|
|
CE1
|
A:HIS558
|
3.0
|
24.2
|
1.0
|
|
HD2
|
A:HIS117
|
3.1
|
26.1
|
1.0
|
|
CE1
|
A:HIS117
|
3.2
|
29.3
|
1.0
|
|
HD2
|
A:HIS558
|
3.2
|
25.1
|
1.0
|
|
CD2
|
A:HIS488
|
3.2
|
23.4
|
1.0
|
|
HE1
|
A:HIS558
|
3.2
|
23.9
|
1.0
|
|
HD2
|
A:HIS486
|
3.2
|
24.7
|
1.0
|
|
HE1
|
A:HIS117
|
3.4
|
29.0
|
1.0
|
|
HD2
|
A:HIS488
|
3.5
|
23.4
|
1.0
|
|
ND1
|
A:HIS488
|
4.0
|
25.3
|
1.0
|
|
ND1
|
A:HIS558
|
4.0
|
23.7
|
1.0
|
|
HB3
|
A:MET556
|
4.1
|
27.3
|
1.0
|
|
CG
|
A:HIS558
|
4.1
|
25.0
|
1.0
|
|
CD2
|
A:HIS486
|
4.1
|
24.4
|
1.0
|
|
CU
|
A:CU712
|
4.1
|
29.8
|
1.0
|
|
HE1
|
A:MET565
|
4.1
|
30.4
|
1.0
|
|
HD2
|
A:HIS69
|
4.1
|
23.8
|
1.0
|
|
HE3
|
A:MET565
|
4.2
|
30.6
|
1.0
|
|
CG
|
A:HIS117
|
4.2
|
26.5
|
1.0
|
|
CG
|
A:HIS488
|
4.2
|
24.0
|
1.0
|
|
ND1
|
A:HIS117
|
4.2
|
28.7
|
1.0
|
|
CD2
|
A:HIS69
|
4.3
|
24.1
|
1.0
|
|
HE2
|
A:HIS486
|
4.3
|
30.0
|
0.0
|
|
HE1
|
A:HIS115
|
4.3
|
24.7
|
1.0
|
|
HE2
|
A:HIS69
|
4.3
|
30.0
|
0.0
|
|
SD
|
A:MET556
|
4.4
|
31.9
|
1.0
|
|
NE2
|
A:HIS69
|
4.4
|
24.1
|
1.0
|
|
O
|
A:HOH1012
|
4.5
|
45.2
|
1.0
|
|
HD2
|
A:HIS560
|
4.5
|
30.0
|
1.0
|
|
NE2
|
A:HIS486
|
4.6
|
25.2
|
1.0
|
|
CE
|
A:MET565
|
4.6
|
30.9
|
1.0
|
|
HD1
|
A:HIS488
|
4.7
|
30.0
|
0.0
|
|
HG23
|
A:THR84
|
4.8
|
29.6
|
1.0
|
|
HD1
|
A:HIS558
|
4.8
|
30.0
|
0.0
|
|
CU
|
A:CU711
|
4.8
|
31.6
|
1.0
|
|
HG2
|
A:MET556
|
4.9
|
29.1
|
1.0
|
|
CG
|
A:HIS69
|
4.9
|
24.4
|
1.0
|
|
CB
|
A:MET556
|
4.9
|
27.6
|
1.0
|
|
HG1
|
A:THR84
|
5.0
|
30.0
|
0.0
|
|
HE2
|
A:HIS560
|
5.0
|
30.0
|
0.0
|
|
CG
|
A:MET556
|
5.0
|
29.0
|
1.0
|
|
Copper binding site 2 out
of 4 in 7zn6
Go back to
Copper Binding Sites List in 7zn6
Copper binding site 2 out
of 4 in the Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu711
b:31.6
occ:1.00
|
HD1
|
A:HIS71
|
1.1
|
30.0
|
0.0
|
|
HE2
|
A:HIS115
|
1.2
|
30.0
|
0.0
|
|
HE2
|
A:HIS560
|
1.5
|
30.0
|
0.0
|
|
ND1
|
A:HIS71
|
2.0
|
25.1
|
1.0
|
|
NE2
|
A:HIS115
|
2.1
|
24.5
|
1.0
|
|
NE2
|
A:HIS560
|
2.3
|
31.5
|
1.0
|
|
O2
|
A:OXY707
|
2.3
|
38.1
|
1.0
|
|
O1
|
A:OXY707
|
2.6
|
32.0
|
1.0
|
|
HB2
|
A:HIS71
|
2.8
|
23.9
|
1.0
|
|
CE1
|
A:HIS71
|
2.9
|
25.0
|
1.0
|
|
HD2
|
A:HIS69
|
3.0
|
23.8
|
1.0
|
|
CG
|
A:HIS71
|
3.0
|
24.4
|
1.0
|
|
HE1
|
A:HIS71
|
3.0
|
24.9
|
1.0
|
|
CE1
|
A:HIS115
|
3.0
|
24.5
|
1.0
|
|
CD2
|
A:HIS115
|
3.1
|
25.7
|
1.0
|
|
HE1
|
A:HIS115
|
3.2
|
24.7
|
1.0
|
|
HD2
|
A:HIS115
|
3.2
|
24.9
|
1.0
|
|
CD2
|
A:HIS560
|
3.3
|
30.0
|
1.0
|
|
CE1
|
A:HIS560
|
3.4
|
30.9
|
1.0
|
|
CB
|
A:HIS71
|
3.4
|
23.6
|
1.0
|
|
HD2
|
A:HIS560
|
3.4
|
30.0
|
1.0
|
|
HE1
|
A:HIS560
|
3.5
|
30.6
|
1.0
|
|
HZ
|
A:PHE113
|
3.7
|
23.2
|
1.0
|
|
CD2
|
A:HIS69
|
3.9
|
24.1
|
1.0
|
|
CU
|
A:CU712
|
4.0
|
29.8
|
1.0
|
|
HB3
|
A:HIS71
|
4.0
|
23.9
|
1.0
|
|
CZ
|
A:PHE113
|
4.0
|
23.7
|
1.0
|
|
NE2
|
A:HIS71
|
4.1
|
24.7
|
1.0
|
|
CD2
|
A:HIS71
|
4.1
|
24.4
|
1.0
|
|
HE2
|
A:HIS486
|
4.1
|
30.0
|
0.0
|
|
ND1
|
A:HIS115
|
4.2
|
24.6
|
1.0
|
|
HD2
|
A:HIS486
|
4.2
|
24.7
|
1.0
|
|
CG
|
A:HIS115
|
4.2
|
24.5
|
1.0
|
|
O
|
A:HOH1012
|
4.3
|
45.2
|
1.0
|
|
HE2
|
A:HIS69
|
4.3
|
30.0
|
0.0
|
|
HA
|
A:HIS71
|
4.3
|
24.0
|
1.0
|
|
NE2
|
A:HIS486
|
4.3
|
25.2
|
1.0
|
|
CD2
|
A:HIS486
|
4.4
|
24.4
|
1.0
|
|
ND1
|
A:HIS560
|
4.5
|
29.6
|
1.0
|
|
CG
|
A:HIS560
|
4.5
|
28.1
|
1.0
|
|
HE1
|
A:PHE113
|
4.5
|
22.7
|
1.0
|
|
HA2
|
A:GLY296
|
4.5
|
22.8
|
1.0
|
|
CE1
|
A:PHE113
|
4.5
|
22.2
|
1.0
|
|
CA
|
A:HIS71
|
4.5
|
24.0
|
1.0
|
|
NE2
|
A:HIS69
|
4.5
|
24.1
|
1.0
|
|
CE2
|
A:PHE113
|
4.6
|
23.8
|
1.0
|
|
HE2
|
A:PHE113
|
4.7
|
23.7
|
1.0
|
|
HD2
|
A:HIS117
|
4.7
|
26.1
|
1.0
|
|
HE2
|
A:HIS71
|
4.8
|
30.0
|
0.0
|
|
CU
|
A:CU710
|
4.8
|
28.5
|
1.0
|
|
HA3
|
A:GLY296
|
4.8
|
22.8
|
1.0
|
|
HE2
|
A:HIS558
|
4.9
|
30.0
|
0.0
|
|
HE1
|
A:HIS558
|
4.9
|
23.9
|
1.0
|
|
HD1
|
A:HIS115
|
4.9
|
30.0
|
0.0
|
|
HD2
|
A:HIS71
|
5.0
|
24.7
|
1.0
|
|
Copper binding site 3 out
of 4 in 7zn6
Go back to
Copper Binding Sites List in 7zn6
Copper binding site 3 out
of 4 in the Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu712
b:29.8
occ:1.00
|
HE2
|
A:HIS486
|
1.1
|
30.0
|
0.0
|
|
HE2
|
A:HIS69
|
1.2
|
30.0
|
0.0
|
|
NE2
|
A:HIS486
|
2.0
|
25.2
|
1.0
|
|
NE2
|
A:HIS69
|
2.0
|
24.1
|
1.0
|
|
O
|
A:HOH996
|
2.8
|
21.6
|
1.0
|
|
O2
|
A:OXY707
|
2.9
|
38.1
|
1.0
|
|
CD2
|
A:HIS69
|
2.9
|
24.1
|
1.0
|
|
CD2
|
A:HIS486
|
2.9
|
24.4
|
1.0
|
|
HA
|
A:HIS71
|
3.0
|
24.0
|
1.0
|
|
CE1
|
A:HIS486
|
3.0
|
23.6
|
1.0
|
|
HD2
|
A:HIS69
|
3.0
|
23.8
|
1.0
|
|
CE1
|
A:HIS69
|
3.0
|
24.7
|
1.0
|
|
HD2
|
A:HIS486
|
3.1
|
24.7
|
1.0
|
|
HE1
|
A:HIS486
|
3.2
|
24.4
|
1.0
|
|
CD2
|
A:HIS488
|
3.2
|
23.4
|
1.0
|
|
NE2
|
A:HIS488
|
3.3
|
23.8
|
1.0
|
|
HE1
|
A:HIS69
|
3.3
|
24.7
|
1.0
|
|
HD2
|
A:HIS488
|
3.4
|
23.4
|
1.0
|
|
HE2
|
A:HIS488
|
3.4
|
30.0
|
0.0
|
|
H
|
A:GLY72
|
3.5
|
24.1
|
1.0
|
|
HD1
|
A:HIS71
|
3.5
|
30.0
|
0.0
|
|
ND1
|
A:HIS71
|
3.6
|
25.1
|
1.0
|
|
HA
|
A:HIS488
|
3.6
|
23.5
|
1.0
|
|
CG
|
A:HIS488
|
3.7
|
24.0
|
1.0
|
|
CE1
|
A:HIS488
|
3.8
|
24.1
|
1.0
|
|
CG
|
A:HIS71
|
3.8
|
24.4
|
1.0
|
|
CA
|
A:HIS71
|
3.9
|
24.0
|
1.0
|
|
CU
|
A:CU711
|
4.0
|
31.6
|
1.0
|
|
O1
|
A:OXY707
|
4.0
|
32.0
|
1.0
|
|
CE1
|
A:HIS71
|
4.0
|
25.0
|
1.0
|
|
CG
|
A:HIS69
|
4.0
|
24.4
|
1.0
|
|
CG
|
A:HIS486
|
4.1
|
24.4
|
1.0
|
|
ND1
|
A:HIS486
|
4.1
|
25.1
|
1.0
|
|
ND1
|
A:HIS488
|
4.1
|
25.3
|
1.0
|
|
CU
|
A:CU710
|
4.1
|
28.5
|
1.0
|
|
ND1
|
A:HIS69
|
4.1
|
24.4
|
1.0
|
|
HB2
|
A:HIS71
|
4.1
|
23.9
|
1.0
|
|
CB
|
A:HIS71
|
4.2
|
23.6
|
1.0
|
|
N
|
A:GLY72
|
4.2
|
23.9
|
1.0
|
|
HE2
|
A:HIS558
|
4.3
|
30.0
|
0.0
|
|
HE1
|
A:HIS488
|
4.3
|
24.4
|
1.0
|
|
HE1
|
A:HIS71
|
4.3
|
24.9
|
1.0
|
|
CD2
|
A:HIS71
|
4.4
|
24.4
|
1.0
|
|
CA
|
A:HIS488
|
4.4
|
23.6
|
1.0
|
|
NE2
|
A:HIS71
|
4.5
|
24.7
|
1.0
|
|
HE2
|
A:HIS115
|
4.5
|
30.0
|
0.0
|
|
C
|
A:HIS71
|
4.6
|
24.2
|
1.0
|
|
CB
|
A:HIS488
|
4.6
|
24.2
|
1.0
|
|
N
|
A:HIS488
|
4.7
|
23.5
|
1.0
|
|
HD1
|
A:HIS488
|
4.7
|
30.0
|
0.0
|
|
O
|
A:ALA487
|
4.8
|
22.9
|
1.0
|
|
N
|
A:HIS71
|
4.9
|
24.0
|
1.0
|
|
HD1
|
A:HIS486
|
4.9
|
30.0
|
0.0
|
|
HD1
|
A:HIS69
|
4.9
|
30.0
|
0.0
|
|
HB3
|
A:HIS488
|
4.9
|
24.3
|
1.0
|
|
HE2
|
A:HIS560
|
4.9
|
30.0
|
0.0
|
|
C
|
A:ALA487
|
5.0
|
23.6
|
1.0
|
|
HD2
|
A:HIS71
|
5.0
|
24.7
|
1.0
|
|
O
|
A:HOH968
|
5.0
|
29.8
|
1.0
|
|
H
|
A:HIS488
|
5.0
|
23.6
|
1.0
|
|
HD2
|
A:HIS560
|
5.0
|
30.0
|
1.0
|
|
Copper binding site 4 out
of 4 in 7zn6
Go back to
Copper Binding Sites List in 7zn6
Copper binding site 4 out
of 4 in the Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Crystal Structure of Laccase-Like Multicopper Oxidase (Lmco) From Thermothelomyces Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu713
b:28.1
occ:1.00
|
HG
|
A:CYS559
|
1.1
|
30.0
|
0.0
|
|
HD1
|
A:HIS483
|
1.2
|
30.0
|
0.0
|
|
HD1
|
A:HIS564
|
1.2
|
30.0
|
0.0
|
|
ND1
|
A:HIS483
|
2.0
|
27.1
|
1.0
|
|
ND1
|
A:HIS564
|
2.1
|
24.6
|
1.0
|
|
SG
|
A:CYS559
|
2.2
|
25.9
|
1.0
|
|
CE1
|
A:HIS483
|
2.9
|
29.4
|
1.0
|
|
HD11
|
A:ILE561
|
3.0
|
27.4
|
1.0
|
|
HB3
|
A:HIS483
|
3.0
|
26.0
|
1.0
|
|
CE1
|
A:HIS564
|
3.1
|
26.4
|
1.0
|
|
HE1
|
A:HIS483
|
3.1
|
29.4
|
1.0
|
|
CG
|
A:HIS483
|
3.1
|
26.9
|
1.0
|
|
CG
|
A:HIS564
|
3.1
|
26.6
|
1.0
|
|
HB2
|
A:CYS559
|
3.1
|
25.8
|
1.0
|
|
CB
|
A:CYS559
|
3.1
|
25.2
|
1.0
|
|
SD
|
A:MET569
|
3.1
|
30.2
|
1.0
|
|
HE1
|
A:HIS564
|
3.2
|
26.1
|
1.0
|
|
HB3
|
A:HIS564
|
3.2
|
26.3
|
1.0
|
|
HB
|
A:ILE561
|
3.2
|
26.4
|
1.0
|
|
HB2
|
A:HIS564
|
3.3
|
25.6
|
1.0
|
|
HB3
|
A:CYS559
|
3.3
|
25.8
|
1.0
|
|
CB
|
A:HIS564
|
3.4
|
26.1
|
1.0
|
|
CB
|
A:HIS483
|
3.5
|
26.3
|
1.0
|
|
HA
|
A:HIS483
|
3.5
|
25.9
|
1.0
|
|
HE1
|
A:MET569
|
3.9
|
30.0
|
1.0
|
|
HD2
|
A:PRO484
|
3.9
|
25.3
|
1.0
|
|
CD1
|
A:ILE561
|
3.9
|
27.2
|
1.0
|
|
CA
|
A:HIS483
|
4.1
|
25.9
|
1.0
|
|
CE
|
A:MET569
|
4.1
|
29.5
|
1.0
|
|
NE2
|
A:HIS483
|
4.1
|
29.9
|
1.0
|
|
CB
|
A:ILE561
|
4.2
|
26.5
|
1.0
|
|
H
|
A:ILE561
|
4.2
|
25.4
|
1.0
|
|
CD2
|
A:HIS483
|
4.2
|
27.9
|
1.0
|
|
NE2
|
A:HIS564
|
4.2
|
26.9
|
1.0
|
|
CD2
|
A:HIS564
|
4.3
|
27.2
|
1.0
|
|
HE2
|
A:MET569
|
4.3
|
29.4
|
1.0
|
|
HB2
|
A:HIS483
|
4.3
|
26.4
|
1.0
|
|
HD12
|
A:ILE561
|
4.4
|
26.9
|
1.0
|
|
CG1
|
A:ILE561
|
4.4
|
26.4
|
1.0
|
|
HD13
|
A:ILE561
|
4.4
|
27.5
|
1.0
|
|
HG13
|
A:ILE561
|
4.5
|
26.0
|
1.0
|
|
HE1
|
A:PHE485
|
4.5
|
28.9
|
1.0
|
|
HG22
|
A:ILE561
|
4.5
|
27.2
|
1.0
|
|
CA
|
A:CYS559
|
4.5
|
25.2
|
1.0
|
|
CG
|
A:MET569
|
4.7
|
28.9
|
1.0
|
|
HB3
|
A:MET569
|
4.7
|
27.6
|
1.0
|
|
HA
|
A:CYS559
|
4.8
|
25.0
|
1.0
|
|
CG2
|
A:ILE561
|
4.8
|
26.6
|
1.0
|
|
CD
|
A:PRO484
|
4.8
|
25.0
|
1.0
|
|
HG2
|
A:MET569
|
4.9
|
28.7
|
1.0
|
|
HE2
|
A:HIS483
|
4.9
|
30.0
|
0.0
|
|
O
|
A:THR482
|
4.9
|
27.5
|
1.0
|
|
HG21
|
A:ILE561
|
4.9
|
27.1
|
1.0
|
|
CA
|
A:HIS564
|
4.9
|
26.9
|
1.0
|
|
HB2
|
A:MET569
|
4.9
|
28.5
|
1.0
|
|
HE3
|
A:MET569
|
4.9
|
30.4
|
1.0
|
|
N
|
A:ILE561
|
5.0
|
25.0
|
1.0
|
|
Reference:
C.Kosinas,
A.Zerva,
E.Topakas,
M.Dimarogona.
Structure-Function Studies of A Novel Laccase-Like Multicopper Oxidase From Thermothelomyces Thermophila Provide Insights Into Its Biological Role. Acta Crystallogr D Struct 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37326583
DOI: 10.1107/S2059798323004175
Page generated: Wed Jul 31 09:30:09 2024
|
