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Copper in PDB 5z0k: Crystal Structure of Copper-Bound Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein Obtained By Soaking in the Hydroxylamine-Containing Solution For 4 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 4 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 4 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 4 H at 277 K, PDB code: 5z0k 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 / 1.28
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.180, 97.600, 54.960, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 18.7

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 4 H at 277 K (pdb code 5z0k). 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 4 H at 277 K, PDB code: 5z0k:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7;

Copper binding site 1 out of 7 in 5z0k

Go back to Copper Binding Sites List in 5z0k
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 4 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 4 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:16.9
occ:0.21
 CU A:CU301 0.0 16.9 0.2
CU A:CU301 1.1 15.2 0.3
NE2 A:HIS38 1.7 14.7 0.5
NE2 A:HIS63 1.8 13.4 1.0
NE2 A:HIS54 2.2 15.3 0.5
O1 A:PER304 2.5 16.5 0.3
CD2 A:HIS38 2.5 14.8 0.5
NE2 A:HIS54 2.5 14.2 0.5
CE1 A:HIS63 2.5 12.7 1.0
CD2 A:HIS38 2.6 14.2 0.5
CE1 A:HIS54 2.6 14.6 0.5
O A:HOH401 2.6 15.9 0.7
NE2 A:HIS38 2.7 14.8 0.5
CU A:CU301 2.8 13.8 0.5
CE1 A:HIS38 2.8 15.2 0.5
CE1 A:HIS54 2.9 14.7 0.5
CD2 A:HIS63 3.1 12.4 1.0
O2 A:PER304 3.2 16.1 0.3
CD2 A:HIS54 3.3 14.6 0.5
CD2 A:HIS54 3.6 13.3 0.5
ND1 A:HIS54 3.7 14.4 0.5
CG A:HIS38 3.7 14.5 0.5
ND1 A:HIS63 3.7 11.3 1.0
ND1 A:HIS38 3.8 14.8 0.5
CG A:HIS38 3.9 13.9 0.5
CE1 A:HIS38 4.0 14.4 0.5
CU A:CU302 4.0 13.7 0.8
CG A:HIS63 4.0 11.0 1.0
ND1 A:HIS54 4.1 14.4 0.5
CZ A:PHE212 4.1 11.9 1.0
CG A:HIS54 4.2 13.6 0.5
CZ3 A:TRP62 4.2 12.8 1.0
CG A:HIS54 4.3 13.8 0.5
OE2 B:DAH98 4.3 17.1 0.5
NE2 A:HIS216 4.3 12.9 1.0
CE2 A:PHE212 4.4 11.3 1.0
ND1 A:HIS38 4.5 13.9 0.5
CE1 A:HIS216 4.6 12.7 1.0
OZ B:DAH98 4.7 16.6 1.0
O A:GLY53 4.7 13.2 1.0
CU A:CU302 4.8 13.8 0.2
CE3 A:TRP62 4.8 12.7 1.0
CB A:HIS38 4.9 13.7 0.5

Copper binding site 2 out of 7 in 5z0k

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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 4 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 4 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:15.2
occ:0.32
 CU A:CU301 0.0 15.2 0.3
CU A:CU301 1.1 16.9 0.2
O1 A:PER304 1.5 16.5 0.3
O A:HOH401 1.8 15.9 0.7
CU A:CU301 1.8 13.8 0.5
NE2 A:HIS38 1.9 14.7 0.5
NE2 A:HIS54 2.0 14.2 0.5
NE2 A:HIS54 2.1 15.3 0.5
O2 A:PER304 2.3 16.1 0.3
NE2 A:HIS38 2.4 14.8 0.5
NE2 A:HIS63 2.5 13.4 1.0
CE1 A:HIS54 2.6 14.6 0.5
CE1 A:HIS38 2.6 15.2 0.5
CD2 A:HIS38 2.9 14.2 0.5
CD2 A:HIS54 3.0 14.6 0.5
CD2 A:HIS54 3.1 13.3 0.5
CE1 A:HIS63 3.1 12.7 1.0
CE1 A:HIS54 3.1 14.7 0.5
CD2 A:HIS38 3.1 14.8 0.5
CU A:CU302 3.2 13.7 0.8
OE2 B:DAH98 3.2 17.1 0.5
CE1 A:HIS38 3.7 14.4 0.5
ND1 A:HIS54 3.7 14.4 0.5
OZ B:DAH98 3.7 16.6 1.0
CD2 A:HIS63 3.7 12.4 1.0
ND1 A:HIS38 3.8 14.8 0.5
CG A:HIS54 4.0 13.6 0.5
NE2 A:HIS216 4.0 12.9 1.0
CU A:CU302 4.0 13.8 0.2
CG A:HIS38 4.1 14.5 0.5
CG A:HIS54 4.2 13.8 0.5
CG A:HIS38 4.2 13.9 0.5
ND1 A:HIS54 4.2 14.4 0.5
CE2 A:PHE212 4.2 11.3 1.0
CZ A:PHE212 4.3 11.9 1.0
ND1 A:HIS63 4.3 11.3 1.0
CE1 A:HIS216 4.4 12.7 1.0
CE2 B:DAH98 4.5 16.6 1.0
ND1 A:HIS38 4.5 13.9 0.5
CZ B:DAH98 4.6 15.9 1.0
CG A:HIS63 4.7 11.0 1.0
NE2 A:HIS190 4.7 13.2 1.0
CD1 A:ILE42 4.8 16.1 0.6
CG1 A:ILE42 4.8 16.5 0.4
CD2 A:HIS216 4.9 13.5 1.0
CE1 A:PHE59 4.9 11.6 1.0
NE2 A:HIS194 4.9 12.6 1.0

Copper binding site 3 out of 7 in 5z0k

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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 4 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 4 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:13.8
occ:0.47
 CU A:CU301 0.0 13.8 0.5
O2 A:PER304 1.8 16.1 0.3
CU A:CU301 1.8 15.2 0.3
O A:HOH401 1.9 15.9 0.7
O1 A:PER304 1.9 16.5 0.3
NE2 A:HIS38 2.0 14.8 0.5
OZ B:DAH98 2.0 16.6 1.0
OE2 B:DAH98 2.1 17.1 0.5
NE2 A:HIS54 2.2 14.2 0.5
CE1 A:HIS38 2.2 15.2 0.5
NE2 A:HIS38 2.6 14.7 0.5
CU A:CU301 2.8 16.9 0.2
NE2 A:HIS54 2.8 15.3 0.5
CE1 A:HIS38 2.8 14.4 0.5
CZ B:DAH98 2.9 15.9 1.0
CE2 B:DAH98 3.1 16.6 1.0
CE1 A:HIS54 3.1 14.6 0.5
CD2 A:HIS54 3.2 13.3 0.5
CD2 A:HIS38 3.2 14.2 0.5
CU A:CU302 3.3 13.7 0.8
CD1 A:ILE42 3.4 16.1 0.6
CD2 A:HIS54 3.5 14.6 0.5
ND1 A:HIS38 3.5 14.8 0.5
CD1 A:ILE42 3.7 18.9 0.4
CE1 A:HIS54 3.8 14.7 0.5
CG1 A:ILE42 3.8 16.5 0.4
CD2 A:HIS38 3.9 14.8 0.5
CU A:CU302 4.0 13.8 0.2
OG A:SER206 4.0 13.5 1.0
ND1 A:HIS38 4.0 13.9 0.5
ND1 A:HIS54 4.2 14.4 0.5
CE1 B:DAH98 4.2 13.8 1.0
CG A:HIS38 4.3 13.9 0.5
CG A:HIS54 4.3 13.6 0.5
NE2 A:HIS194 4.3 12.6 1.0
NE2 A:HIS63 4.3 13.4 1.0
CG1 A:ILE42 4.3 16.1 0.6
CE1 A:HIS194 4.3 13.4 1.0
CG A:HIS38 4.4 14.5 0.5
CD2 B:DAH98 4.4 15.4 1.0
CE2 A:PHE212 4.5 11.3 1.0
CG A:HIS54 4.6 13.8 0.5
O B:HOH374 4.7 25.6 1.0
ND1 A:HIS54 4.7 14.4 0.5
NE2 A:HIS190 4.8 13.2 1.0
NE2 A:HIS216 4.8 12.9 1.0
CE1 A:HIS63 4.8 12.7 1.0
CB A:ILE42 4.9 15.5 0.6
CE1 A:HIS190 4.9 12.2 1.0
CZ A:PHE212 5.0 11.9 1.0

Copper binding site 4 out of 7 in 5z0k

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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 4 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 4 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:13.8
occ:0.21
 CU A:CU302 0.0 13.8 0.2
CU A:CU302 1.0 13.7 0.8
NE2 A:HIS194 1.7 12.6 1.0
NE2 A:HIS216 1.9 12.9 1.0
NE2 A:HIS190 2.3 13.2 1.0
O2 A:PER304 2.3 16.1 0.3
O A:HOH401 2.4 15.9 0.7
CE1 A:HIS194 2.6 13.4 1.0
CD2 A:HIS216 2.7 13.5 1.0
O1 A:PER304 2.7 16.5 0.3
CD2 A:HIS194 2.8 11.9 1.0
CD2 A:HIS190 3.0 11.8 1.0
CE1 A:HIS216 3.0 12.7 1.0
CE1 A:HIS190 3.4 12.2 1.0
OE2 B:DAH98 3.6 17.1 0.5
ND1 A:HIS194 3.8 12.0 1.0
CD2 A:HIS215 3.8 13.6 1.0
CG A:HIS216 3.9 11.2 1.0
CG A:HIS194 3.9 12.0 1.0
CE2 A:PHE212 4.0 11.3 1.0
CU A:CU301 4.0 15.2 0.3
ND1 A:HIS216 4.0 12.0 1.0
CU A:CU301 4.0 13.8 0.5
NE2 A:HIS215 4.1 14.2 1.0
CG A:HIS190 4.2 11.7 1.0
CE2 B:DAH98 4.2 16.6 1.0
OZ B:DAH98 4.3 16.6 1.0
ND1 A:HIS190 4.3 12.1 1.0
CZ B:DAH98 4.5 15.9 1.0
CD2 A:PHE212 4.5 11.9 1.0
CZ A:PHE212 4.6 11.9 1.0
CU A:CU301 4.8 16.9 0.2
NE2 A:HIS63 4.9 13.4 1.0
CG A:HIS215 5.0 11.9 1.0
CD2 B:DAH98 5.0 15.4 1.0

Copper binding site 5 out of 7 in 5z0k

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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 4 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 4 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:13.7
occ:0.79
 CU A:CU302 0.0 13.7 0.8
CU A:CU302 1.0 13.8 0.2
O A:HOH401 1.7 15.9 0.7
O1 A:PER304 1.8 16.5 0.3
O2 A:PER304 1.8 16.1 0.3
NE2 A:HIS190 2.0 13.2 1.0
NE2 A:HIS216 2.1 12.9 1.0
NE2 A:HIS194 2.2 12.6 1.0
OE2 B:DAH98 2.8 17.1 0.5
CE1 A:HIS190 2.9 12.2 1.0
CE1 A:HIS216 3.0 12.7 1.0
CD2 A:HIS190 3.1 11.8 1.0
CE1 A:HIS194 3.2 13.4 1.0
CU A:CU301 3.2 15.2 0.3
CD2 A:HIS194 3.2 11.9 1.0
CD2 A:HIS216 3.2 13.5 1.0
CU A:CU301 3.3 13.8 0.5
CE2 B:DAH98 3.7 16.6 1.0
OZ B:DAH98 3.9 16.6 1.0
CU A:CU301 4.0 16.9 0.2
ND1 A:HIS190 4.0 12.1 1.0
CZ B:DAH98 4.1 15.9 1.0
CG A:HIS190 4.2 11.7 1.0
ND1 A:HIS216 4.2 12.0 1.0
CE2 A:PHE212 4.2 11.3 1.0
NE2 A:HIS63 4.3 13.4 1.0
ND1 A:HIS194 4.3 12.0 1.0
NE2 A:HIS54 4.3 14.2 0.5
CG A:HIS216 4.3 11.2 1.0
CG A:HIS194 4.3 12.0 1.0
CD2 B:DAH98 4.5 15.4 1.0
CE1 A:PHE59 4.5 11.6 1.0
NE2 A:HIS38 4.5 14.7 0.5
CD2 A:HIS54 4.6 13.3 0.5
CZ A:PHE212 4.8 11.9 1.0
NE2 A:HIS38 4.8 14.8 0.5
NE2 A:HIS54 4.8 15.3 0.5
CD2 A:HIS215 4.8 13.6 1.0
CE1 A:HIS63 4.8 12.7 1.0
CD2 A:HIS63 4.8 12.4 1.0
CE1 A:HIS38 4.8 15.2 0.5
NE2 A:HIS215 4.9 14.2 1.0
CZ A:PHE59 4.9 12.1 1.0
CD2 A:HIS54 4.9 14.6 0.5

Copper binding site 6 out of 7 in 5z0k

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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 4 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 4 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu303

b:52.2
occ:0.50
 NE2 A:HIS277 1.8 49.0 1.0
O A:HOH537 2.2 39.9 0.5
CE1 A:HIS277 2.6 49.2 1.0
O A:HOH619 2.6 32.0 0.5
CD2 A:HIS277 3.0 49.5 1.0
ND1 A:HIS277 3.8 49.3 1.0
O A:HOH679 3.8 58.4 1.0
CG A:HIS277 4.0 50.4 1.0
CG A:PRO231 4.6 23.7 1.0
O A:HOH427 4.8 39.5 1.0

Copper binding site 7 out of 7 in 5z0k

Go back to Copper Binding Sites List in 5z0k
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 4 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 4 H at 277 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:22.5
occ:1.00
 NE2 B:HIS82 1.9 22.0 1.0
NE2 B:HIS97 2.0 25.4 1.0
SD B:MET84 2.2 22.6 1.0
CE1 B:HIS97 2.9 23.5 1.0
CE1 B:HIS82 2.9 20.7 1.0
CD2 B:HIS82 2.9 21.4 1.0
CG B:MET84 3.0 22.2 1.0
CD2 B:HIS97 3.2 25.3 1.0
CE B:MET84 3.3 22.1 1.0
O A:ILE42 3.3 17.4 1.0
CB B:MET84 3.6 18.1 1.0
CA A:MET43 3.8 17.7 1.0
ND1 B:HIS82 4.0 21.3 1.0
O A:MET43 4.0 24.2 1.0
CG B:HIS82 4.1 19.5 1.0
ND1 B:HIS97 4.1 20.7 1.0
C A:ILE42 4.2 17.5 1.0
C A:MET43 4.3 18.8 1.0
CG B:HIS97 4.3 21.4 1.0
N A:MET43 4.4 16.0 1.0
CG2 A:ILE42 4.5 17.6 0.4
CG A:MET43 4.7 17.7 1.0
O A:HOH428 4.7 26.1 1.0
CB A:MET43 4.7 17.2 1.0
N B:MET84 4.8 14.1 1.0
CA B:MET84 4.8 15.3 1.0
C B:VAL83 4.9 13.8 1.0
O B:VAL83 5.0 16.8 1.0
CG1 B:ILE92 5.0 16.3 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 05:29:54 2024

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