Copper in PDB 5z0e: Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K
Enzymatic activity of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K
All present enzymatic activity of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K:
1.14.18.1;
Protein crystallography data
The structure of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K, PDB code: 5z0e
was solved by
Y.Matoba,
M.Sugiyama,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.16
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.630,
96.930,
54.510,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
13.1 /
17
|
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K
(pdb code 5z0e). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the
Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K, PDB code: 5z0e:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 5z0e
Go back to
Copper Binding Sites List in 5z0e
Copper binding site 1 out
of 6 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K
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 Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu301
b:13.6
occ:0.65
|
CU
|
A:CU301
|
0.0
|
13.6
|
0.7
|
CU
|
A:CU301
|
1.0
|
18.0
|
0.3
|
NE2
|
A:HIS38
|
1.9
|
13.9
|
1.0
|
NE2
|
A:HIS63
|
1.9
|
11.1
|
1.0
|
NE2
|
A:HIS54
|
2.1
|
14.7
|
1.0
|
O
|
A:HOH401
|
2.6
|
12.8
|
0.7
|
CE1
|
A:HIS63
|
2.8
|
10.7
|
1.0
|
O2
|
A:PER303
|
2.8
|
12.6
|
0.3
|
CD2
|
A:HIS38
|
2.8
|
14.5
|
1.0
|
O1
|
A:PER303
|
2.8
|
11.9
|
0.3
|
CE1
|
A:HIS38
|
2.9
|
14.1
|
1.0
|
CE1
|
A:HIS54
|
3.1
|
15.2
|
1.0
|
CD2
|
A:HIS63
|
3.1
|
10.9
|
1.0
|
CD2
|
A:HIS54
|
3.1
|
16.0
|
1.0
|
CG
|
A:HIS38
|
3.9
|
13.6
|
1.0
|
ND1
|
A:HIS38
|
4.0
|
14.4
|
1.0
|
ND1
|
A:HIS63
|
4.0
|
9.3
|
1.0
|
CG
|
A:HIS63
|
4.2
|
9.6
|
1.0
|
ND1
|
A:HIS54
|
4.2
|
15.3
|
1.0
|
CZ
|
A:PHE212
|
4.2
|
10.1
|
1.0
|
CU
|
A:CU302
|
4.2
|
12.4
|
0.3
|
CG
|
A:HIS54
|
4.2
|
14.2
|
1.0
|
NE2
|
A:HIS216
|
4.3
|
10.7
|
1.0
|
CZ3
|
A:TRP62
|
4.4
|
12.5
|
1.0
|
CE2
|
A:PHE212
|
4.4
|
9.5
|
1.0
|
CU
|
A:CU302
|
4.4
|
13.4
|
0.7
|
CE1
|
A:HIS216
|
4.6
|
10.8
|
1.0
|
CD1
|
A:ILE42
|
4.6
|
17.5
|
1.0
|
CE3
|
A:TRP62
|
4.9
|
10.5
|
1.0
|
CG1
|
A:ILE42
|
4.9
|
14.7
|
1.0
|
O
|
A:GLY53
|
4.9
|
11.3
|
1.0
|
|
Copper binding site 2 out
of 6 in 5z0e
Go back to
Copper Binding Sites List in 5z0e
Copper binding site 2 out
of 6 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K
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 Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu301
b:18.0
occ:0.35
|
CU
|
A:CU301
|
0.0
|
18.0
|
0.3
|
CU
|
A:CU301
|
1.0
|
13.6
|
0.7
|
O
|
A:HOH401
|
1.6
|
12.8
|
0.7
|
O1
|
A:PER303
|
1.9
|
11.9
|
0.3
|
O2
|
A:PER303
|
1.9
|
12.6
|
0.3
|
NE2
|
A:HIS54
|
2.1
|
14.7
|
1.0
|
NE2
|
A:HIS38
|
2.2
|
13.9
|
1.0
|
NE2
|
A:HIS63
|
2.5
|
11.1
|
1.0
|
CE1
|
A:HIS38
|
2.9
|
14.1
|
1.0
|
CD2
|
A:HIS54
|
2.9
|
16.0
|
1.0
|
CE1
|
A:HIS63
|
3.2
|
10.7
|
1.0
|
CE1
|
A:HIS54
|
3.3
|
15.2
|
1.0
|
CD2
|
A:HIS38
|
3.4
|
14.5
|
1.0
|
CU
|
A:CU302
|
3.5
|
12.4
|
0.3
|
CD2
|
A:HIS63
|
3.7
|
10.9
|
1.0
|
CU
|
A:CU302
|
3.7
|
13.4
|
0.7
|
NE2
|
A:HIS216
|
4.0
|
10.7
|
1.0
|
ND1
|
A:HIS38
|
4.1
|
14.4
|
1.0
|
CG
|
A:HIS54
|
4.1
|
14.2
|
1.0
|
CD1
|
A:ILE42
|
4.1
|
17.5
|
1.0
|
ND1
|
A:HIS54
|
4.3
|
15.3
|
1.0
|
CE2
|
A:PHE212
|
4.3
|
9.5
|
1.0
|
CG
|
A:HIS38
|
4.4
|
13.6
|
1.0
|
CE1
|
A:HIS216
|
4.4
|
10.8
|
1.0
|
CZ
|
A:PHE212
|
4.4
|
10.1
|
1.0
|
ND1
|
A:HIS63
|
4.5
|
9.3
|
1.0
|
CG1
|
A:ILE42
|
4.7
|
14.7
|
1.0
|
CG
|
A:HIS63
|
4.8
|
9.6
|
1.0
|
NE2
|
A:HIS190
|
4.8
|
10.6
|
1.0
|
CE1
|
A:PHE59
|
4.9
|
9.5
|
1.0
|
CZ
|
B:PHE98
|
4.9
|
12.8
|
1.0
|
|
Copper binding site 3 out
of 6 in 5z0e
Go back to
Copper Binding Sites List in 5z0e
Copper binding site 3 out
of 6 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K
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 Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu302
b:13.4
occ:0.65
|
CU
|
A:CU302
|
0.0
|
13.4
|
0.7
|
CU
|
A:CU302
|
0.5
|
12.4
|
0.3
|
NE2
|
A:HIS216
|
1.9
|
10.7
|
1.0
|
NE2
|
A:HIS194
|
2.0
|
9.9
|
1.0
|
NE2
|
A:HIS190
|
2.0
|
10.6
|
1.0
|
O2
|
A:PER303
|
2.1
|
12.6
|
0.3
|
O
|
A:HOH401
|
2.5
|
12.8
|
0.7
|
O1
|
A:PER303
|
2.6
|
11.9
|
0.3
|
CE1
|
A:HIS216
|
2.8
|
10.8
|
1.0
|
CD2
|
A:HIS190
|
3.0
|
9.9
|
1.0
|
CD2
|
A:HIS216
|
3.0
|
10.2
|
1.0
|
CE1
|
A:HIS194
|
3.0
|
9.5
|
1.0
|
CE1
|
A:HIS190
|
3.1
|
10.0
|
1.0
|
CD2
|
A:HIS194
|
3.1
|
9.8
|
1.0
|
CU
|
A:CU301
|
3.7
|
18.0
|
0.3
|
ND1
|
A:HIS216
|
4.0
|
9.8
|
1.0
|
CG
|
A:HIS216
|
4.1
|
9.3
|
1.0
|
CE2
|
A:PHE212
|
4.1
|
9.5
|
1.0
|
CG
|
A:HIS190
|
4.1
|
9.6
|
1.0
|
ND1
|
A:HIS190
|
4.2
|
9.8
|
1.0
|
ND1
|
A:HIS194
|
4.2
|
9.2
|
1.0
|
CD2
|
A:HIS215
|
4.2
|
11.3
|
1.0
|
CG
|
A:HIS194
|
4.2
|
8.9
|
1.0
|
NE2
|
A:HIS215
|
4.4
|
11.4
|
1.0
|
CU
|
A:CU301
|
4.4
|
13.6
|
0.7
|
CE2
|
B:PHE98
|
4.5
|
13.1
|
1.0
|
CZ
|
B:PHE98
|
4.6
|
12.8
|
1.0
|
NE2
|
A:HIS63
|
4.7
|
11.1
|
1.0
|
CD2
|
A:PHE212
|
4.7
|
9.3
|
1.0
|
CZ
|
A:PHE212
|
4.7
|
10.1
|
1.0
|
CE1
|
A:PHE59
|
4.9
|
9.5
|
1.0
|
|
Copper binding site 4 out
of 6 in 5z0e
Go back to
Copper Binding Sites List in 5z0e
Copper binding site 4 out
of 6 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K
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 Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu302
b:12.4
occ:0.35
|
CU
|
A:CU302
|
0.0
|
12.4
|
0.3
|
CU
|
A:CU302
|
0.5
|
13.4
|
0.7
|
O2
|
A:PER303
|
1.7
|
12.6
|
0.3
|
NE2
|
A:HIS194
|
1.9
|
9.9
|
1.0
|
NE2
|
A:HIS190
|
2.1
|
10.6
|
1.0
|
O
|
A:HOH401
|
2.1
|
12.8
|
0.7
|
O1
|
A:PER303
|
2.2
|
11.9
|
0.3
|
NE2
|
A:HIS216
|
2.3
|
10.7
|
1.0
|
CE1
|
A:HIS194
|
2.9
|
9.5
|
1.0
|
CE1
|
A:HIS190
|
3.0
|
10.0
|
1.0
|
CD2
|
A:HIS194
|
3.0
|
9.8
|
1.0
|
CD2
|
A:HIS190
|
3.2
|
9.9
|
1.0
|
CE1
|
A:HIS216
|
3.2
|
10.8
|
1.0
|
CD2
|
A:HIS216
|
3.4
|
10.2
|
1.0
|
CU
|
A:CU301
|
3.5
|
18.0
|
0.3
|
ND1
|
A:HIS194
|
4.0
|
9.2
|
1.0
|
CE2
|
B:PHE98
|
4.0
|
13.1
|
1.0
|
CG
|
A:HIS194
|
4.1
|
8.9
|
1.0
|
CZ
|
B:PHE98
|
4.1
|
12.8
|
1.0
|
ND1
|
A:HIS190
|
4.1
|
9.8
|
1.0
|
CE2
|
A:PHE212
|
4.1
|
9.5
|
1.0
|
CU
|
A:CU301
|
4.2
|
13.6
|
0.7
|
CG
|
A:HIS190
|
4.3
|
9.6
|
1.0
|
ND1
|
A:HIS216
|
4.4
|
9.8
|
1.0
|
CG
|
A:HIS216
|
4.5
|
9.3
|
1.0
|
CD2
|
A:HIS215
|
4.6
|
11.3
|
1.0
|
NE2
|
A:HIS63
|
4.7
|
11.1
|
1.0
|
NE2
|
A:HIS215
|
4.7
|
11.4
|
1.0
|
CD2
|
A:PHE212
|
4.8
|
9.3
|
1.0
|
CZ
|
A:PHE212
|
4.9
|
10.1
|
1.0
|
NE2
|
A:HIS38
|
4.9
|
13.9
|
1.0
|
CD2
|
B:PHE98
|
4.9
|
12.6
|
1.0
|
CE1
|
A:PHE59
|
4.9
|
9.5
|
1.0
|
OG
|
A:SER206
|
5.0
|
11.4
|
1.0
|
|
Copper binding site 5 out
of 6 in 5z0e
Go back to
Copper Binding Sites List in 5z0e
Copper binding site 5 out
of 6 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu201
b:17.4
occ:0.43
|
O1
|
B:NO3202
|
1.8
|
17.0
|
0.6
|
CE
|
B:MET84
|
1.8
|
26.2
|
0.6
|
NE2
|
B:HIS82
|
2.0
|
15.8
|
0.4
|
N
|
B:NO3202
|
2.1
|
15.9
|
0.6
|
NE2
|
B:HIS97
|
2.1
|
16.0
|
0.4
|
SD
|
B:MET84
|
2.3
|
18.3
|
0.4
|
O3
|
B:NO3202
|
2.7
|
16.8
|
0.6
|
O2
|
B:NO3202
|
2.8
|
15.0
|
0.6
|
SD
|
B:MET84
|
2.8
|
23.4
|
0.6
|
CE1
|
B:HIS82
|
2.9
|
16.5
|
0.4
|
CE
|
B:MET84
|
3.0
|
17.7
|
0.4
|
CE1
|
B:HIS97
|
3.0
|
15.9
|
0.4
|
CG
|
B:MET84
|
3.0
|
17.9
|
0.4
|
CD2
|
B:HIS82
|
3.0
|
15.7
|
0.4
|
O
|
A:ILE42
|
3.1
|
14.5
|
1.0
|
CD2
|
B:HIS97
|
3.2
|
14.1
|
0.4
|
CB
|
B:MET84
|
3.3
|
17.9
|
0.6
|
CB
|
B:MET84
|
3.4
|
17.5
|
0.4
|
CE1
|
B:HIS97
|
3.5
|
15.3
|
0.6
|
CG
|
B:MET84
|
3.7
|
19.8
|
0.6
|
CE1
|
B:HIS82
|
3.7
|
16.7
|
0.6
|
ND1
|
B:HIS82
|
3.7
|
15.1
|
0.6
|
ND1
|
B:HIS97
|
3.8
|
13.9
|
0.6
|
CA
|
A:MET43
|
3.9
|
15.0
|
1.0
|
ND1
|
B:HIS82
|
4.1
|
16.0
|
0.4
|
C
|
A:ILE42
|
4.1
|
13.7
|
1.0
|
ND1
|
B:HIS97
|
4.1
|
15.6
|
0.4
|
O
|
A:MET43
|
4.2
|
17.6
|
1.0
|
CG
|
B:HIS82
|
4.2
|
15.1
|
0.4
|
CG
|
B:HIS97
|
4.3
|
14.9
|
0.4
|
C
|
A:MET43
|
4.4
|
13.6
|
1.0
|
O
|
A:HOH416
|
4.4
|
19.0
|
1.0
|
N
|
A:MET43
|
4.5
|
13.3
|
1.0
|
CG2
|
A:ILE42
|
4.6
|
14.9
|
1.0
|
CA
|
B:MET84
|
4.6
|
13.9
|
1.0
|
NE2
|
B:HIS97
|
4.7
|
16.1
|
0.6
|
N
|
B:MET84
|
4.7
|
12.0
|
1.0
|
CD1
|
B:ILE92
|
4.7
|
14.5
|
1.0
|
CG1
|
B:ILE92
|
4.8
|
13.6
|
1.0
|
C
|
B:VAL83
|
4.9
|
12.0
|
1.0
|
CB
|
A:MET43
|
4.9
|
17.3
|
1.0
|
O
|
B:VAL83
|
5.0
|
14.4
|
1.0
|
|
Copper binding site 6 out
of 6 in 5z0e
Go back to
Copper Binding Sites List in 5z0e
Copper binding site 6 out
of 6 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Y98F Mutant of the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 2 H at 298 K within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu201
b:43.4
occ:0.57
|
NE2
|
B:HIS82
|
2.2
|
18.2
|
0.6
|
CD2
|
B:HIS82
|
3.0
|
17.2
|
0.6
|
CE1
|
B:HIS82
|
3.2
|
16.7
|
0.6
|
O
|
A:HOH601
|
3.4
|
48.0
|
1.0
|
ND1
|
B:HIS82
|
3.7
|
16.0
|
0.4
|
CE1
|
B:HIS82
|
4.0
|
16.5
|
0.4
|
CG
|
B:HIS82
|
4.2
|
14.6
|
0.6
|
ND1
|
B:HIS82
|
4.2
|
15.1
|
0.6
|
O
|
A:MET43
|
4.3
|
17.6
|
1.0
|
O
|
B:HOH366
|
4.8
|
20.5
|
1.0
|
CG
|
B:HIS82
|
5.0
|
15.1
|
0.4
|
|
Reference:
Y.Matoba,
M.Sugiyama.
Catalytic Mechanism of Tyrosinase Implied From the Quinone Formation on the TYR98 Residue of the Caddie Protein To Be Published.
Page generated: Wed Jul 31 05:26:27 2024
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