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Copper in PDB 5z0i: Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 1 H at 277 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 1 H at 277 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 1 H at 277 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 1 H at 277 K, PDB code: 5z0i 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 / 1.32
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 64.930, 97.330, 54.840, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 18.8

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 1 H at 277 K (pdb code 5z0i). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 7 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 1 H at 277 K, PDB code: 5z0i:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7;

Copper binding site 1 out of 7 in 5z0i

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Copper binding site 1 out of 7 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 1 H at 277 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 1 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:15.8
occ:0.50
CU A:CU301 0.0 15.8 0.5
CU A:CU301 1.2 14.8 0.4
NE2 A:HIS38 1.9 15.9 0.9
NE2 A:HIS63 1.9 14.4 1.0
NE2 A:HIS54 2.2 16.9 0.9
CE1 A:HIS54 2.3 16.5 0.1
NE2 A:HIS54 2.3 16.5 0.1
NE2 A:HIS38 2.5 15.7 0.1
CU A:CU301 2.6 15.9 0.1
O A:HOH401 2.6 15.8 0.6
CD2 A:HIS38 2.7 16.0 0.9
CE1 A:HIS63 2.7 13.7 1.0
O1 A:PER304 2.7 16.2 0.4
CD2 A:HIS38 2.8 15.7 0.1
O2 A:PER304 2.9 15.9 0.4
CE1 A:HIS54 3.0 16.7 0.9
CE1 A:HIS38 3.0 15.8 0.9
CD2 A:HIS63 3.1 12.9 1.0
CD2 A:HIS54 3.3 16.8 0.9
ND1 A:HIS54 3.5 16.3 0.1
CD2 A:HIS54 3.6 16.3 0.1
CE1 A:HIS38 3.8 15.4 0.1
CG A:HIS38 3.9 15.6 0.9
ND1 A:HIS63 3.9 13.4 1.0
ND1 A:HIS38 4.0 15.1 0.9
CU A:CU302 4.0 13.2 0.5
CG A:HIS38 4.0 15.4 0.1
CG A:HIS63 4.1 13.3 1.0
CZ A:PHE212 4.1 12.9 1.0
ND1 A:HIS54 4.1 16.7 0.9
CG A:HIS54 4.2 15.8 0.1
CZ3 A:TRP62 4.3 14.9 1.0
NE2 A:HIS216 4.3 13.6 1.0
CG A:HIS54 4.3 15.4 0.9
CE2 A:PHE212 4.4 13.1 1.0
CU A:CU302 4.4 13.8 0.5
ND1 A:HIS38 4.5 15.1 0.1
CE1 A:HIS216 4.6 13.7 1.0
OZ B:DAH98 4.6 16.5 1.0
OE2 B:DAH98 4.7 14.5 0.1
CE3 A:TRP62 4.9 13.7 1.0
O A:GLY53 4.9 15.7 1.0

Copper binding site 2 out of 7 in 5z0i

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Copper binding site 2 out of 7 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 1 H at 277 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 1 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:14.8
occ:0.38
CU A:CU301 0.0 14.8 0.4
CU A:CU301 1.2 15.8 0.5
CU A:CU301 1.5 15.9 0.1
NE2 A:HIS54 1.7 16.5 0.1
O1 A:PER304 1.7 16.2 0.4
O A:HOH401 1.8 15.8 0.6
O2 A:PER304 2.0 15.9 0.4
NE2 A:HIS54 2.0 16.9 0.9
NE2 A:HIS38 2.2 15.9 0.9
CE1 A:HIS54 2.3 16.5 0.1
NE2 A:HIS38 2.6 15.7 0.1
NE2 A:HIS63 2.6 14.4 1.0
CD2 A:HIS54 2.9 16.8 0.9
CE1 A:HIS38 2.9 15.8 0.9
CD2 A:HIS54 3.0 16.3 0.1
CE1 A:HIS54 3.2 16.7 0.9
CU A:CU302 3.2 13.2 0.5
CE1 A:HIS63 3.2 13.7 1.0
CD2 A:HIS38 3.3 15.7 0.1
CD2 A:HIS38 3.4 16.0 0.9
ND1 A:HIS54 3.5 16.3 0.1
OE2 B:DAH98 3.5 14.5 0.1
CE1 A:HIS38 3.6 15.4 0.1
OZ B:DAH98 3.7 16.5 1.0
CU A:CU302 3.7 13.8 0.5
CD2 A:HIS63 3.8 12.9 1.0
CG A:HIS54 3.9 15.8 0.1
NE2 A:HIS216 4.1 13.6 1.0
CG A:HIS54 4.1 15.4 0.9
ND1 A:HIS38 4.1 15.1 0.9
ND1 A:HIS54 4.2 16.7 0.9
CG A:HIS38 4.4 15.6 0.9
CE2 A:PHE212 4.4 13.1 1.0
CE2 B:DAH98 4.5 16.2 1.0
CD1 A:ILE42 4.5 25.1 1.0
ND1 A:HIS63 4.5 13.4 1.0
CE1 A:HIS216 4.5 13.7 1.0
CG A:HIS38 4.5 15.4 0.1
CZ A:PHE212 4.5 12.9 1.0
CZ B:DAH98 4.6 15.5 1.0
ND1 A:HIS38 4.6 15.1 0.1
CG1 A:ILE42 4.6 22.8 1.0
NE2 A:HIS190 4.7 13.5 1.0
CG A:HIS63 4.8 13.3 1.0
CE1 A:PHE59 4.9 13.5 1.0
NE2 A:HIS194 5.0 12.9 1.0

Copper binding site 3 out of 7 in 5z0i

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Copper binding site 3 out of 7 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 1 H at 277 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 1 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:15.9
occ:0.12
CU A:CU301 0.0 15.9 0.1
O2 A:PER304 1.5 15.9 0.4
CU A:CU301 1.5 14.8 0.4
O A:HOH401 1.7 15.8 0.6
O1 A:PER304 1.8 16.2 0.4
OZ B:DAH98 2.2 16.5 1.0
NE2 A:HIS54 2.3 16.5 0.1
NE2 A:HIS38 2.4 15.7 0.1
CE1 A:HIS38 2.4 15.8 0.9
NE2 A:HIS38 2.5 15.9 0.9
CU A:CU301 2.6 15.8 0.5
OE2 B:DAH98 2.6 14.5 0.1
NE2 A:HIS54 2.8 16.9 0.9
CE1 A:HIS38 2.9 15.4 0.1
CE1 A:HIS54 3.1 16.5 0.1
CZ B:DAH98 3.1 15.5 1.0
CU A:CU302 3.1 13.2 0.5
CE2 B:DAH98 3.2 16.2 1.0
CD2 A:HIS54 3.3 16.3 0.1
CD2 A:HIS54 3.4 16.8 0.9
CD1 A:ILE42 3.5 25.1 1.0
CD2 A:HIS38 3.6 15.7 0.1
CU A:CU302 3.6 13.8 0.5
ND1 A:HIS38 3.8 15.1 0.9
CE1 A:HIS54 3.9 16.7 0.9
CD2 A:HIS38 3.9 16.0 0.9
CG1 A:ILE42 3.9 22.8 1.0
NE2 A:HIS63 4.1 14.4 1.0
ND1 A:HIS38 4.2 15.1 0.1
OG A:SER206 4.2 13.4 1.0
ND1 A:HIS54 4.2 16.3 0.1
NE2 A:HIS194 4.3 12.9 1.0
CG A:HIS54 4.4 15.8 0.1
CE1 A:HIS194 4.4 12.8 1.0
CE2 A:PHE212 4.4 13.1 1.0
CE1 B:DAH98 4.4 14.4 1.0
CG A:HIS38 4.5 15.6 0.9
CG A:HIS38 4.5 15.4 0.1
CD2 B:DAH98 4.6 16.1 1.0
CG A:HIS54 4.6 15.4 0.9
NE2 A:HIS216 4.6 13.6 1.0
NE2 A:HIS190 4.7 13.5 1.0
CE1 A:HIS63 4.8 13.7 1.0
O B:HOH369 4.8 28.3 1.0
ND1 A:HIS54 4.8 16.7 0.9
CE1 A:HIS190 4.9 13.7 1.0
CZ A:PHE212 5.0 12.9 1.0

Copper binding site 4 out of 7 in 5z0i

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Copper binding site 4 out of 7 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 1 H at 277 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 1 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:13.8
occ:0.50
CU A:CU302 0.0 13.8 0.5
CU A:CU302 0.8 13.2 0.5
NE2 A:HIS194 1.9 12.9 1.0
NE2 A:HIS216 1.9 13.6 1.0
NE2 A:HIS190 2.1 13.5 1.0
O A:HOH401 2.2 15.8 0.6
O2 A:PER304 2.3 15.9 0.4
O1 A:PER304 2.5 16.2 0.4
CE1 A:HIS194 2.8 12.8 1.0
CD2 A:HIS216 2.9 12.5 1.0
CE1 A:HIS216 2.9 13.7 1.0
CD2 A:HIS190 3.0 13.4 1.0
CD2 A:HIS194 3.0 12.8 1.0
CE1 A:HIS190 3.2 13.7 1.0
OE2 B:DAH98 3.6 14.5 0.1
CU A:CU301 3.6 15.9 0.1
CU A:CU301 3.7 14.8 0.4
ND1 A:HIS194 4.0 12.0 1.0
CG A:HIS216 4.0 12.2 1.0
ND1 A:HIS216 4.0 12.5 1.0
OZ B:DAH98 4.1 16.5 1.0
CE2 A:PHE212 4.1 13.1 1.0
CE2 B:DAH98 4.1 16.2 1.0
CG A:HIS194 4.1 12.2 1.0
CD2 A:HIS215 4.1 13.9 1.0
CG A:HIS190 4.2 13.5 1.0
ND1 A:HIS190 4.3 14.2 1.0
NE2 A:HIS215 4.4 15.3 1.0
CZ B:DAH98 4.4 15.5 1.0
CU A:CU301 4.4 15.8 0.5
NE2 A:HIS63 4.7 14.4 1.0
CD2 A:PHE212 4.7 12.8 1.0
CZ A:PHE212 4.7 12.9 1.0
NE2 A:HIS54 4.8 16.5 0.1
CD2 B:DAH98 5.0 16.1 1.0
NE2 A:HIS38 5.0 15.7 0.1

Copper binding site 5 out of 7 in 5z0i

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Copper binding site 5 out of 7 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 1 H at 277 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 1 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:13.2
occ:0.50
CU A:CU302 0.0 13.2 0.5
CU A:CU302 0.8 13.8 0.5
O1 A:PER304 1.8 16.2 0.4
O A:HOH401 1.8 15.8 0.6
O2 A:PER304 1.9 15.9 0.4
NE2 A:HIS190 2.0 13.5 1.0
NE2 A:HIS194 2.2 12.9 1.0
NE2 A:HIS216 2.3 13.6 1.0
CE1 A:HIS190 2.8 13.7 1.0
OE2 B:DAH98 2.9 14.5 0.1
CE1 A:HIS216 3.1 13.7 1.0
CU A:CU301 3.1 15.9 0.1
CD2 A:HIS190 3.1 13.4 1.0
CE1 A:HIS194 3.2 12.8 1.0
CU A:CU301 3.2 14.8 0.4
CD2 A:HIS194 3.2 12.8 1.0
CD2 A:HIS216 3.4 12.5 1.0
CE2 B:DAH98 3.6 16.2 1.0
OZ B:DAH98 3.8 16.5 1.0
ND1 A:HIS190 4.0 14.2 1.0
CU A:CU301 4.0 15.8 0.5
CZ B:DAH98 4.0 15.5 1.0
NE2 A:HIS54 4.1 16.5 0.1
CG A:HIS190 4.2 13.5 1.0
ND1 A:HIS194 4.3 12.0 1.0
ND1 A:HIS216 4.3 12.5 1.0
CG A:HIS194 4.3 12.2 1.0
NE2 A:HIS63 4.4 14.4 1.0
CE2 A:PHE212 4.4 13.1 1.0
CG A:HIS216 4.5 12.2 1.0
CD2 B:DAH98 4.5 16.1 1.0
CE1 A:PHE59 4.6 13.5 1.0
CD2 A:HIS54 4.6 16.3 0.1
NE2 A:HIS38 4.7 15.7 0.1
NE2 A:HIS38 4.8 15.9 0.9
CD2 A:HIS215 4.8 13.9 1.0
NE2 A:HIS54 4.9 16.9 0.9
CD2 A:HIS63 4.9 12.9 1.0
NE2 A:HIS215 4.9 15.3 1.0
CZ A:PHE212 5.0 12.9 1.0
CD2 A:HIS54 5.0 16.8 0.9
CE1 A:HIS63 5.0 13.7 1.0
O A:HOH504 5.0 18.5 1.0
CZ A:PHE59 5.0 14.4 1.0

Copper binding site 6 out of 7 in 5z0i

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Copper binding site 6 out of 7 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 1 H at 277 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 1 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu303

b:62.7
occ:0.50
O A:HOH681 2.4 33.7 0.5
CG A:PRO231 4.9 29.6 1.0
O A:HOH452 4.9 42.3 1.0

Copper binding site 7 out of 7 in 5z0i

Go back to Copper Binding Sites List in 5z0i
Copper binding site 7 out of 7 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 1 H at 277 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 1 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:23.1
occ:1.00
NE2 B:HIS82 2.0 23.0 1.0
NE2 B:HIS97 2.1 24.3 1.0
SD B:MET84 2.2 25.4 1.0
CD2 B:HIS82 3.0 22.4 1.0
CE1 B:HIS82 3.0 21.9 1.0
CE1 B:HIS97 3.0 22.0 1.0
CD2 B:HIS97 3.1 24.2 1.0
CG B:MET84 3.1 24.4 1.0
CE B:MET84 3.2 26.1 1.0
O A:ILE42 3.2 19.3 1.0
CB B:MET84 3.5 20.0 1.0
CA A:MET43 3.8 19.7 1.0
O A:MET43 4.0 23.8 1.0
ND1 B:HIS82 4.1 20.7 1.0
C A:ILE42 4.1 18.0 1.0
CG B:HIS82 4.1 20.0 1.0
ND1 B:HIS97 4.2 20.0 1.0
C A:MET43 4.2 20.1 1.0
CG B:HIS97 4.3 20.0 1.0
N A:MET43 4.4 18.2 1.0
CG2 A:ILE42 4.5 24.6 1.0
O A:HOH442 4.6 20.6 1.0
CA B:MET84 4.7 16.8 1.0
N B:MET84 4.8 16.3 1.0
CD1 B:ILE92 4.8 28.9 1.0
CB A:MET43 4.9 20.6 1.0
CG1 B:ILE92 4.9 18.9 1.0
CG A:MET43 4.9 21.8 1.0
C B:VAL83 5.0 15.6 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: Wed Jul 31 05:29:06 2024

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