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Copper in PDB 5z0f: Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K

Enzymatic activity of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K

All present enzymatic activity of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min 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 Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K, PDB code: 5z0f 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 (°) 64.650, 96.990, 54.870, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 16

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K (pdb code 5z0f). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K, PDB code: 5z0f:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 5z0f

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Copper binding site 1 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min 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 Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:11.7
occ:0.58
CU A:CU301 0.0 11.7 0.6
CU A:CU301 1.2 14.2 0.3
NE2 A:HIS38 1.8 12.7 0.9
NE2 A:HIS63 1.9 10.1 1.0
NE2 A:HIS54 2.0 13.8 0.1
NE2 A:HIS54 2.1 13.7 0.9
NE2 A:HIS38 2.2 13.2 0.1
CE1 A:HIS54 2.4 13.5 0.1
O A:HOH401 2.5 14.7 0.6
CD2 A:HIS38 2.6 13.1 0.1
O1 A:PER304 2.7 14.5 0.4
CU A:CU301 2.7 14.2 0.1
CE1 A:HIS63 2.8 9.3 1.0
CD2 A:HIS38 2.8 13.7 0.9
O2 A:PER304 2.8 14.5 0.4
CE1 A:HIS38 2.9 13.0 0.9
CE1 A:HIS54 3.1 13.4 0.9
CD2 A:HIS63 3.1 9.4 1.0
CD2 A:HIS54 3.1 13.6 0.9
CD2 A:HIS54 3.2 13.5 0.1
CE1 A:HIS38 3.4 12.9 0.1
ND1 A:HIS54 3.6 13.0 0.1
CG A:HIS38 3.9 12.7 0.9
CG A:HIS38 3.9 12.6 0.1
ND1 A:HIS38 4.0 13.0 0.9
ND1 A:HIS63 4.0 8.7 1.0
CG A:HIS54 4.0 12.9 0.1
CU A:CU302 4.0 11.9 0.4
CG A:HIS63 4.2 8.2 1.0
CZ A:PHE212 4.2 10.2 1.0
ND1 A:HIS54 4.2 12.1 0.9
CG A:HIS54 4.3 12.2 0.9
ND1 A:HIS38 4.3 12.5 0.1
NE2 A:HIS216 4.3 10.6 1.0
CE2 A:PHE212 4.4 10.4 1.0
CZ3 A:TRP62 4.4 11.5 1.0
CU A:CU302 4.5 11.6 0.6
CE1 A:HIS216 4.6 9.4 1.0
CD1 A:ILE42 4.7 21.2 1.0
OE2 B:DAH98 4.7 11.7 0.0
OZ B:DAH98 4.7 15.6 1.0
CG1 A:ILE42 4.9 16.9 1.0
CE3 A:TRP62 4.9 10.0 1.0
O A:GLY53 4.9 9.9 1.0

Copper binding site 2 out of 8 in 5z0f

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Copper binding site 2 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min 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 Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:14.2
occ:0.29
CU A:CU301 0.0 14.2 0.3
CU A:CU301 1.2 11.7 0.6
O A:HOH401 1.5 14.7 0.6
NE2 A:HIS54 1.7 13.8 0.1
CU A:CU301 1.7 14.2 0.1
O2 A:PER304 1.7 14.5 0.4
O1 A:PER304 1.8 14.5 0.4
NE2 A:HIS54 2.2 13.7 0.9
NE2 A:HIS38 2.2 12.7 0.9
NE2 A:HIS38 2.3 13.2 0.1
CE1 A:HIS54 2.6 13.5 0.1
NE2 A:HIS63 2.7 10.1 1.0
CD2 A:HIS54 2.7 13.5 0.1
CE1 A:HIS38 2.8 13.0 0.9
CD2 A:HIS54 2.9 13.6 0.9
CU A:CU302 3.2 11.9 0.4
CE1 A:HIS38 3.2 12.9 0.1
CD2 A:HIS38 3.2 13.1 0.1
CE1 A:HIS63 3.4 9.3 1.0
CE1 A:HIS54 3.4 13.4 0.9
CD2 A:HIS38 3.5 13.7 0.9
OE2 B:DAH98 3.5 11.7 0.0
ND1 A:HIS54 3.7 13.0 0.1
CU A:CU302 3.7 11.6 0.6
OZ B:DAH98 3.7 15.6 1.0
CG A:HIS54 3.8 12.9 0.1
CD2 A:HIS63 3.9 9.4 1.0
CD1 A:ILE42 4.1 21.2 1.0
NE2 A:HIS216 4.1 10.6 1.0
ND1 A:HIS38 4.1 13.0 0.9
CG A:HIS54 4.1 12.2 0.9
ND1 A:HIS54 4.3 12.1 0.9
ND1 A:HIS38 4.4 12.5 0.1
CE2 A:PHE212 4.4 10.4 1.0
CG A:HIS38 4.4 12.6 0.1
CG A:HIS38 4.4 12.7 0.9
CE1 A:HIS216 4.5 9.4 1.0
CZ A:PHE212 4.5 10.2 1.0
CG1 A:ILE42 4.6 16.9 1.0
CE2 B:DAH98 4.6 14.8 1.0
ND1 A:HIS63 4.6 8.7 1.0
NE2 A:HIS190 4.6 9.3 1.0
CZ B:DAH98 4.7 13.6 1.0
CE1 A:PHE59 4.8 9.3 1.0
NE2 A:HIS194 4.9 8.7 1.0
CG A:HIS63 4.9 8.2 1.0
CE1 A:HIS190 5.0 9.3 1.0

Copper binding site 3 out of 8 in 5z0f

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Copper binding site 3 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min 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 Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:14.2
occ:0.13
CU A:CU301 0.0 14.2 0.1
CU A:CU301 1.7 14.2 0.3
O A:HOH401 1.7 14.7 0.6
O1 A:PER304 2.0 14.5 0.4
O2 A:PER304 2.1 14.5 0.4
OZ B:DAH98 2.3 15.6 1.0
NE2 A:HIS54 2.3 13.8 0.1
NE2 A:HIS38 2.3 13.2 0.1
CE1 A:HIS38 2.4 13.0 0.9
CE1 A:HIS38 2.6 12.9 0.1
OE2 B:DAH98 2.6 11.7 0.0
CU A:CU301 2.7 11.7 0.6
NE2 A:HIS38 2.7 12.7 0.9
CD1 A:ILE42 2.9 21.2 1.0
NE2 A:HIS54 2.9 13.7 0.9
CD2 A:HIS54 3.1 13.5 0.1
CZ B:DAH98 3.2 13.6 1.0
CE1 A:HIS54 3.3 13.5 0.1
CD2 A:HIS54 3.4 13.6 0.9
CE2 B:DAH98 3.4 14.8 1.0
CU A:CU302 3.5 11.9 0.4
CG1 A:ILE42 3.6 16.9 1.0
CD2 A:HIS38 3.7 13.1 0.1
ND1 A:HIS38 3.7 13.0 0.9
ND1 A:HIS38 3.9 12.5 0.1
CE1 A:HIS54 3.9 13.4 0.9
CU A:CU302 4.0 11.6 0.6
CD2 A:HIS38 4.1 13.7 0.9
O B:HOH355 4.2 32.5 1.0
CG A:HIS54 4.2 12.9 0.1
OG A:SER206 4.2 9.6 1.0
ND1 A:HIS54 4.3 13.0 0.1
NE2 A:HIS63 4.4 10.1 1.0
CG A:HIS38 4.4 12.6 0.1
CG A:HIS54 4.5 12.2 0.9
CE1 B:DAH98 4.5 12.1 1.0
CG A:HIS38 4.5 12.7 0.9
NE2 A:HIS194 4.5 8.7 1.0
CE1 A:HIS194 4.6 8.8 1.0
CE2 A:PHE212 4.7 10.4 1.0
ND1 A:HIS54 4.7 12.1 0.9
CD2 B:DAH98 4.8 13.7 1.0
NE2 A:HIS190 5.0 9.3 1.0
CE1 A:HIS63 5.0 9.3 1.0

Copper binding site 4 out of 8 in 5z0f

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Copper binding site 4 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min 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 Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:11.6
occ:0.58
CU A:CU302 0.0 11.6 0.6
CU A:CU302 0.7 11.9 0.4
NE2 A:HIS194 1.9 8.7 1.0
NE2 A:HIS216 1.9 10.6 1.0
NE2 A:HIS190 2.1 9.3 1.0
O1 A:PER304 2.2 14.5 0.4
O A:HOH401 2.4 14.7 0.6
O2 A:PER304 2.5 14.5 0.4
CE1 A:HIS194 2.8 8.8 1.0
CD2 A:HIS216 2.9 10.6 1.0
CE1 A:HIS216 2.9 9.4 1.0
CD2 A:HIS194 3.0 8.3 1.0
CD2 A:HIS190 3.0 8.8 1.0
CE1 A:HIS190 3.2 9.3 1.0
OE2 B:DAH98 3.7 11.7 0.0
CU A:CU301 3.7 14.2 0.3
ND1 A:HIS194 4.0 8.8 1.0
CE2 A:PHE212 4.0 10.4 1.0
ND1 A:HIS216 4.0 8.9 1.0
CU A:CU301 4.0 14.2 0.1
CG A:HIS216 4.1 8.5 1.0
CD2 A:HIS215 4.1 10.6 1.0
CG A:HIS194 4.1 8.0 1.0
CG A:HIS190 4.2 8.6 1.0
OZ B:DAH98 4.2 15.6 1.0
ND1 A:HIS190 4.3 9.4 1.0
CE2 B:DAH98 4.3 14.8 1.0
NE2 A:HIS215 4.3 10.3 1.0
CU A:CU301 4.5 11.7 0.6
CZ B:DAH98 4.5 13.6 1.0
CD2 A:PHE212 4.6 9.5 1.0
CZ A:PHE212 4.7 10.2 1.0
NE2 A:HIS63 4.8 10.1 1.0

Copper binding site 5 out of 8 in 5z0f

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Copper binding site 5 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min 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 Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:11.9
occ:0.42
CU A:CU302 0.0 11.9 0.4
CU A:CU302 0.7 11.6 0.6
O1 A:PER304 1.9 14.5 0.4
O2 A:PER304 1.9 14.5 0.4
NE2 A:HIS190 1.9 9.3 1.0
O A:HOH401 1.9 14.7 0.6
NE2 A:HIS194 2.2 8.7 1.0
NE2 A:HIS216 2.2 10.6 1.0
CE1 A:HIS190 2.8 9.3 1.0
CE1 A:HIS216 3.0 9.4 1.0
CD2 A:HIS190 3.0 8.8 1.0
OE2 B:DAH98 3.1 11.7 0.0
CE1 A:HIS194 3.2 8.8 1.0
CD2 A:HIS194 3.2 8.3 1.0
CU A:CU301 3.2 14.2 0.3
CD2 A:HIS216 3.4 10.6 1.0
CU A:CU301 3.5 14.2 0.1
CE2 B:DAH98 3.9 14.8 1.0
OZ B:DAH98 3.9 15.6 1.0
ND1 A:HIS190 4.0 9.4 1.0
CU A:CU301 4.0 11.7 0.6
CG A:HIS190 4.1 8.6 1.0
CZ B:DAH98 4.2 13.6 1.0
ND1 A:HIS216 4.3 8.9 1.0
ND1 A:HIS194 4.3 8.8 1.0
CE2 A:PHE212 4.3 10.4 1.0
CG A:HIS194 4.3 8.0 1.0
NE2 A:HIS54 4.5 13.8 0.1
CG A:HIS216 4.5 8.5 1.0
NE2 A:HIS63 4.5 10.1 1.0
CE1 A:PHE59 4.6 9.3 1.0
CD2 A:HIS54 4.7 13.5 0.1
CD2 A:HIS215 4.7 10.6 1.0
NE2 A:HIS38 4.8 13.2 0.1
CD2 B:DAH98 4.8 13.7 1.0
NE2 A:HIS215 4.8 10.3 1.0
NE2 A:HIS38 4.9 12.7 0.9
CZ A:PHE59 4.9 8.9 1.0
CZ A:PHE212 4.9 10.2 1.0
CD2 A:HIS63 5.0 9.4 1.0

Copper binding site 6 out of 8 in 5z0f

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Copper binding site 6 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min 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 Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu303

b:35.6
occ:0.50
NE2 A:HIS277 1.9 37.5 1.0
NE2 A:HIS279 2.4 56.1 1.0
O A:HOH563 2.5 24.7 0.5
CD2 A:HIS277 2.9 38.6 1.0
CE1 A:HIS277 2.9 37.8 1.0
CE1 A:HIS279 3.3 54.2 1.0
CD2 A:HIS279 3.5 57.6 1.0
ND1 A:HIS277 4.0 38.7 1.0
CG A:HIS277 4.1 39.4 1.0
O A:HOH546 4.3 36.9 1.0
ND1 A:HIS279 4.4 55.2 1.0
CG A:HIS279 4.6 57.2 1.0
CG A:PRO231 4.9 22.8 1.0

Copper binding site 7 out of 8 in 5z0f

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Copper binding site 7 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:22.7
occ:0.64
OE1 B:GLU67 1.9 34.0 1.0
O B:HIS68 2.0 36.1 1.0
NE2 B:HIS82 2.0 18.5 0.6
ND1 B:HIS68 2.1 31.1 1.0
O B:HOH374 2.5 37.9 1.0
N B:HIS68 2.7 29.5 1.0
CD2 B:HIS82 2.9 17.5 0.6
C B:HIS68 2.9 35.6 1.0
CE1 B:HIS68 3.0 31.1 1.0
CE1 B:HIS82 3.1 16.7 0.6
CD B:GLU67 3.1 34.5 1.0
CG B:HIS68 3.2 31.6 1.0
CA B:HIS68 3.2 33.2 1.0
C B:GLU67 3.3 31.4 1.0
CB B:GLU67 3.4 33.7 1.0
ND1 B:HIS82 3.4 16.2 0.4
CE1 B:HIS82 3.6 16.0 0.4
CB B:HIS68 3.6 33.0 1.0
CA B:GLU67 3.9 31.6 1.0
CG B:GLU67 3.9 35.9 1.0
O B:GLU67 4.0 34.4 1.0
OE2 B:GLU67 4.0 35.0 1.0
CG B:HIS82 4.1 15.0 0.6
O A:MET43 4.1 17.2 1.0
ND1 B:HIS82 4.1 14.9 0.6
N B:GLY69 4.2 38.6 1.0
NE2 B:HIS68 4.2 31.3 1.0
CD2 B:HIS68 4.3 30.7 1.0
N B:GLY70 4.4 47.1 1.0
O B:HOH368 4.6 22.6 1.0
CA B:GLY69 4.7 41.5 1.0
CA B:GLY70 4.7 46.0 1.0
CG B:HIS82 4.8 14.2 0.4
NE2 B:HIS82 4.9 15.8 0.4
C B:GLY69 5.0 46.1 1.0

Copper binding site 8 out of 8 in 5z0f

Go back to Copper Binding Sites List in 5z0f
Copper binding site 8 out of 8 in the Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 10 Min at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:15.8
occ:0.36
CE B:MET84 1.7 18.8 0.6
O1 B:NO3202 2.0 25.0 0.6
NE2 B:HIS82 2.1 15.8 0.4
NE2 B:HIS97 2.2 15.3 0.4
SD B:MET84 2.2 16.6 0.4
N B:NO3202 2.3 15.0 0.6
CG B:MET84 2.3 16.9 0.4
O3 B:NO3202 2.8 19.2 0.6
SD B:MET84 2.9 19.8 0.6
O2 B:NO3202 3.0 16.5 0.6
CD2 B:HIS82 3.1 14.3 0.4
CE1 B:HIS82 3.1 16.0 0.4
CE1 B:HIS97 3.1 14.9 0.4
CD2 B:HIS97 3.2 14.2 0.4
CB B:MET84 3.2 17.1 0.6
O A:ILE42 3.3 14.4 1.0
CB B:MET84 3.3 17.0 0.4
CG B:MET84 3.6 18.9 0.6
CE1 B:HIS82 3.7 16.7 0.6
CE1 B:HIS97 3.7 14.8 0.6
ND1 B:HIS82 3.7 14.9 0.6
CA A:MET43 3.7 14.2 1.0
CE B:MET84 3.8 18.9 0.4
ND1 B:HIS97 4.0 12.8 0.6
O A:MET43 4.1 17.2 1.0
ND1 B:HIS82 4.2 16.2 0.4
C A:ILE42 4.2 12.3 1.0
C A:MET43 4.2 13.1 1.0
CG B:HIS82 4.3 14.2 0.4
ND1 B:HIS97 4.3 14.2 0.4
CG B:HIS97 4.4 13.7 0.4
N A:MET43 4.4 12.7 1.0
CA B:MET84 4.6 13.2 1.0
O A:HOH450 4.6 17.6 1.0
N B:MET84 4.7 11.8 1.0
CB A:MET43 4.7 15.4 1.0
CG2 A:ILE42 4.8 18.1 1.0
CD1 B:ILE92 4.8 18.5 1.0
C B:VAL83 4.9 11.3 1.0
NE2 B:HIS97 4.9 15.5 0.6
CG1 B:ILE92 4.9 14.8 1.0
CG A:MET43 4.9 17.9 1.0
NE2 B:HIS82 5.0 18.5 0.6
O B:VAL83 5.0 14.2 1.0

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: Mon Jul 14 05:37:52 2025

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