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Copper in PDB 5z0d: 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein

Enzymatic activity of 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein

All present enzymatic activity of 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein:
1.14.18.1;

Protein crystallography data

The structure of 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein, PDB code: 5z0d 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 (°) 64.660, 97.010, 54.830, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 16

Copper Binding Sites:

The binding sites of Copper atom in the 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein (pdb code 5z0d). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein, PDB code: 5z0d:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 5z0d

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Copper binding site 1 out of 5 in the 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu301

b:12.2
occ:1.00
 NE2 A:HIS63 1.9 9.1 1.0
NE2 A:HIS38 1.9 10.6 1.0
NE2 A:HIS54 2.1 10.5 1.0
O B:HOH366 2.6 10.9 1.0
CE1 A:HIS63 2.9 8.6 1.0
CD2 A:HIS38 2.9 11.1 1.0
CE1 A:HIS38 3.0 10.7 1.0
CD2 A:HIS54 3.1 10.8 1.0
CD2 A:HIS63 3.1 8.4 1.0
CE1 A:HIS54 3.1 10.5 1.0
ND1 A:HIS63 4.0 8.0 1.0
CG A:HIS38 4.1 10.4 1.0
ND1 A:HIS38 4.1 10.7 1.0
CZ A:PHE212 4.1 11.1 1.0
CG A:HIS63 4.2 7.5 1.0
ND1 A:HIS54 4.2 10.6 1.0
CG A:HIS54 4.2 9.9 1.0
CU A:CU302 4.3 11.2 1.0
CE2 A:PHE212 4.4 11.7 1.0
NE2 A:HIS216 4.4 9.1 1.0
CZ3 A:TRP62 4.4 10.4 1.0
CE1 A:HIS216 4.5 9.1 1.0
CD1 A:ILE42 4.6 14.1 1.0
OH B:TYR98 4.8 14.0 1.0
CE3 A:TRP62 4.9 9.0 1.0
CG1 A:ILE42 5.0 12.6 1.0

Copper binding site 2 out of 5 in 5z0d

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Copper binding site 2 out of 5 in the 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:11.2
occ:1.00
 NE2 A:HIS194 2.0 7.9 1.0
NE2 A:HIS216 2.0 9.1 1.0
NE2 A:HIS190 2.0 8.9 1.0
O B:HOH366 2.4 10.9 1.0
CE1 A:HIS216 2.9 9.1 1.0
CE1 A:HIS194 3.0 8.9 1.0
CD2 A:HIS190 3.0 8.4 1.0
CE1 A:HIS190 3.0 9.1 1.0
CD2 A:HIS216 3.1 8.9 1.0
CD2 A:HIS194 3.1 8.1 1.0
CE2 A:PHE212 4.0 11.7 1.0
ND1 A:HIS216 4.1 8.2 1.0
ND1 A:HIS194 4.1 8.6 1.0
CG A:HIS216 4.1 7.3 1.0
CG A:HIS190 4.2 8.6 1.0
ND1 A:HIS190 4.2 9.4 1.0
CG A:HIS194 4.2 7.6 1.0
OH B:TYR98 4.2 14.0 1.0
CD2 A:HIS215 4.3 9.2 1.0
CU A:CU301 4.3 12.2 1.0
CE2 B:TYR98 4.3 11.9 1.0
NE2 A:HIS215 4.5 9.8 1.0
CZ B:TYR98 4.5 11.5 1.0
CD2 A:PHE212 4.7 10.9 1.0
CZ A:PHE212 4.7 11.1 1.0
NE2 A:HIS63 4.7 9.1 1.0
CE1 A:PHE59 5.0 8.8 1.0

Copper binding site 3 out of 5 in 5z0d

Go back to Copper Binding Sites List in 5z0d
Copper binding site 3 out of 5 in the 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu303

b:61.0
occ:0.50
 NE2 A:HIS277 2.0 80.7 1.0
CD2 A:HIS277 2.8 80.7 1.0
O A:HOH587 3.0 32.7 0.5
CE1 A:HIS277 3.2 80.6 1.0
CG A:HIS277 4.1 79.9 1.0
ND1 A:HIS277 4.2 80.2 1.0
O A:HOH671 4.2 53.8 1.0
O A:HOH556 4.7 42.5 1.0
CG A:PRO231 4.8 22.5 1.0

Copper binding site 4 out of 5 in 5z0d

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Copper binding site 4 out of 5 in the 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:25.9
occ:0.75
 OE1 B:GLU67 1.9 36.9 1.0
O B:HIS68 2.0 45.1 1.0
NE2 B:HIS82 2.1 15.7 0.8
ND1 B:HIS68 2.5 44.6 1.0
N B:HIS68 2.5 40.4 1.0
O B:HOH365 2.6 41.7 1.0
C B:HIS68 2.9 45.4 1.0
CD2 B:HIS82 3.0 14.2 0.8
CA B:HIS68 3.1 43.5 1.0
CD B:GLU67 3.1 38.5 1.0
CE1 B:HIS82 3.2 13.9 0.8
CB B:GLU67 3.2 41.7 1.0
C B:GLU67 3.2 39.0 1.0
CE1 B:HIS68 3.3 43.2 1.0
CG B:HIS68 3.3 44.7 1.0
ND1 B:HIS82 3.4 14.1 0.2
CE1 B:HIS82 3.6 13.9 0.2
CB B:HIS68 3.6 42.3 1.0
CG B:GLU67 3.8 43.9 1.0
CA B:GLU67 3.8 38.4 1.0
O B:GLU67 3.9 36.8 1.0
O A:MET43 4.0 18.0 1.0
OE2 B:GLU67 4.1 41.5 1.0
N B:GLY69 4.1 46.2 1.0
CG B:HIS82 4.2 12.2 0.8
ND1 B:HIS82 4.2 12.5 0.8
NE2 B:HIS68 4.3 44.1 1.0
CD2 B:HIS68 4.4 44.6 1.0
O B:HOH360 4.7 19.9 1.0
CA B:GLY69 4.8 48.2 1.0
CA B:GLY70 4.8 48.6 1.0
CG B:HIS82 4.8 12.3 0.2
NE2 B:HIS82 4.9 14.1 0.2
N B:GLU67 5.0 41.4 1.0

Copper binding site 5 out of 5 in 5z0d

Go back to Copper Binding Sites List in 5z0d
Copper binding site 5 out of 5 in the 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of 1.16 A-Resolution Crystal Structure of the Deoxy-Form Tyrosinase From Streptomyces Castaneoglobisporus in Complex with the Caddie Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:25.4
occ:0.25
 O1 B:NO3202 1.8 30.8 0.8
N B:NO3202 1.9 27.6 0.8
O3 B:NO3202 2.2 24.1 0.8
SD B:MET84 2.2 19.0 0.2
NE2 B:HIS97 2.2 14.6 0.2
NE2 B:HIS82 2.4 14.1 0.2
CE B:MET84 2.5 22.5 0.8
O2 B:NO3202 2.7 21.8 0.8
CG B:MET84 2.8 17.2 0.2
SD B:MET84 3.0 19.4 0.8
CE B:MET84 3.0 11.9 0.2
CD2 B:HIS97 3.1 12.2 0.2
O A:ILE42 3.2 12.9 1.0
CD2 B:HIS82 3.2 13.2 0.2
CE1 B:HIS97 3.3 14.4 0.2
CB B:MET84 3.4 17.6 0.8
CE1 B:HIS82 3.5 13.9 0.2
CB B:MET84 3.5 16.6 0.2
CE1 B:HIS97 3.5 14.2 0.8
ND1 B:HIS97 3.8 12.5 0.8
CG B:MET84 3.8 18.9 0.8
ND1 B:HIS82 3.9 12.5 0.8
CE1 B:HIS82 3.9 13.9 0.8
CA A:MET43 4.0 13.5 1.0
C A:ILE42 4.1 11.6 1.0
CG B:HIS97 4.3 12.8 0.2
ND1 B:HIS97 4.3 14.0 0.2
CG2 A:ILE42 4.4 12.8 1.0
CG B:HIS82 4.5 12.3 0.2
O A:HOH455 4.5 15.3 1.0
N A:MET43 4.5 12.3 1.0
O A:MET43 4.5 18.0 1.0
ND1 B:HIS82 4.5 14.1 0.2
C A:MET43 4.6 13.6 1.0
CD1 B:ILE92 4.6 15.2 1.0
CA B:MET84 4.7 12.4 1.0
CG1 B:ILE92 4.7 12.5 1.0
N B:MET84 4.7 10.5 1.0
NE2 B:HIS97 4.8 14.4 0.8
C B:VAL83 5.0 10.4 1.0
CB A:MET43 5.0 15.1 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 05:26:14 2024

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