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Copper in PDB 2zwg: Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours

Enzymatic activity of Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours

All present enzymatic activity of Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours:
1.14.18.1;

Protein crystallography data

The structure of Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours, PDB code: 2zwg 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 (°) 65.240, 97.760, 55.070, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.5

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours (pdb code 2zwg). 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 the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours, PDB code: 2zwg:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2zwg

Go back to Copper Binding Sites List in 2zwg
Copper binding site 1 out of 6 in the Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours


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 the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:12.0
occ:0.73
 CU A:CU501 0.0 12.0 0.7
CU A:CU501 1.8 9.2 0.3
O A:HOH530 1.9 12.1 1.0
O B:HOH546 1.9 14.7 1.0
NE2 A:HIS38 2.0 10.9 0.7
NE2 A:HIS54 2.1 13.8 1.0
NE2 A:HIS63 2.5 8.3 1.0
NE2 A:HIS38 2.6 10.1 0.3
CE1 A:HIS38 3.0 10.1 0.7
CD2 A:HIS54 3.0 12.1 1.0
CD2 A:HIS38 3.0 9.6 0.3
CD2 A:HIS38 3.1 8.7 0.7
CE1 A:HIS54 3.1 12.0 1.0
CE1 A:HIS63 3.1 7.3 1.0
OE2 B:DAH98 3.2 15.6 0.7
CU A:CU502 3.2 15.4 1.0
CD2 A:HIS63 3.7 9.1 1.0
OZ B:DAH98 3.7 13.1 1.0
CE1 A:HIS38 3.8 9.8 0.3
NE2 A:HIS216 4.0 9.4 1.0
ND1 A:HIS38 4.1 9.8 0.7
CG A:HIS54 4.1 9.7 1.0
CG A:HIS38 4.2 9.4 0.7
ND1 A:HIS54 4.2 10.3 1.0
ND1 A:HIS63 4.4 7.4 1.0
CG A:HIS38 4.4 8.8 0.3
CE2 A:PHE212 4.4 9.2 1.0
CE2 B:DAH98 4.4 9.9 1.0
CZ A:PHE212 4.4 9.2 1.0
CE1 A:HIS216 4.4 10.3 1.0
CZ B:DAH98 4.6 12.7 1.0
NE2 A:HIS190 4.6 7.3 1.0
CG A:HIS63 4.7 6.5 1.0
ND1 A:HIS38 4.7 9.6 0.3
CD1 A:ILE42 4.7 16.1 1.0
NE2 A:HIS194 4.8 7.3 1.0
CE1 A:PHE59 4.8 8.8 1.0
CE1 A:HIS190 4.9 9.6 1.0
CD2 A:HIS216 5.0 8.8 1.0

Copper binding site 2 out of 6 in 2zwg

Go back to Copper Binding Sites List in 2zwg
Copper binding site 2 out of 6 in the Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours


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 the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:9.2
occ:0.27
 CU A:CU501 0.0 9.2 0.3
CU A:CU501 1.8 12.0 0.7
O A:HOH530 2.1 12.1 1.0
NE2 A:HIS38 2.1 10.1 0.3
OZ B:DAH98 2.1 13.1 1.0
OE2 B:DAH98 2.2 15.6 0.7
NE2 A:HIS38 2.2 10.9 0.7
CE1 A:HIS38 2.3 10.1 0.7
NE2 A:HIS54 2.6 13.8 1.0
O B:HOH546 2.7 14.7 1.0
CE1 A:HIS38 2.9 9.8 0.3
CZ B:DAH98 3.0 12.7 1.0
CE2 B:DAH98 3.0 9.9 1.0
CD2 A:HIS38 3.3 9.6 0.3
CD1 A:ILE42 3.3 16.1 1.0
CD2 A:HIS54 3.3 12.1 1.0
CU A:CU502 3.5 15.4 1.0
CE1 A:HIS54 3.6 12.0 1.0
CD2 A:HIS38 3.6 8.7 0.7
ND1 A:HIS38 3.6 9.8 0.7
ND1 A:HIS38 4.1 9.6 0.3
CG1 A:ILE42 4.1 18.2 1.0
OG A:SER206 4.2 8.7 1.0
CG A:HIS38 4.3 9.4 0.7
CG A:HIS38 4.3 8.8 0.3
NE2 A:HIS63 4.3 8.3 1.0
CE1 B:DAH98 4.3 9.4 1.0
CD2 B:DAH98 4.4 10.0 1.0
NE2 A:HIS194 4.4 7.3 1.0
CG A:HIS54 4.4 9.7 1.0
CE1 A:HIS194 4.5 7.7 1.0
ND1 A:HIS54 4.6 10.3 1.0
O B:HOH558 4.6 15.8 1.0
CB A:ILE42 4.6 17.6 1.0
CE2 A:PHE212 4.7 9.2 1.0
CE1 A:HIS63 4.8 7.3 1.0
NE2 A:HIS190 4.9 7.3 1.0
NE2 A:HIS216 5.0 9.4 1.0

Copper binding site 3 out of 6 in 2zwg

Go back to Copper Binding Sites List in 2zwg
Copper binding site 3 out of 6 in the Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours


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 the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:15.4
occ:1.00
 NE2 A:HIS190 1.9 7.3 1.0
O A:HOH530 2.0 12.1 1.0
NE2 A:HIS194 2.1 7.3 1.0
NE2 A:HIS216 2.2 9.4 1.0
O B:HOH546 2.3 14.7 1.0
CE1 A:HIS190 2.9 9.6 1.0
CE1 A:HIS216 3.0 10.3 1.0
CD2 A:HIS190 3.0 8.2 1.0
CE1 A:HIS194 3.0 7.7 1.0
OE2 B:DAH98 3.1 15.6 0.7
CD2 A:HIS194 3.1 7.8 1.0
CU A:CU501 3.2 12.0 0.7
CD2 A:HIS216 3.3 8.8 1.0
CU A:CU501 3.5 9.2 0.3
CE2 B:DAH98 3.7 9.9 1.0
OZ B:DAH98 4.0 13.1 1.0
ND1 A:HIS190 4.0 8.4 1.0
CG A:HIS190 4.1 7.5 1.0
ND1 A:HIS194 4.2 8.9 1.0
CZ B:DAH98 4.2 12.7 1.0
ND1 A:HIS216 4.2 8.6 1.0
CG A:HIS194 4.2 9.2 1.0
CE2 A:PHE212 4.3 9.2 1.0
CG A:HIS216 4.3 8.3 1.0
NE2 A:HIS63 4.4 8.3 1.0
CD2 B:DAH98 4.6 10.0 1.0
CD2 A:HIS215 4.6 9.7 1.0
CE1 A:PHE59 4.6 8.8 1.0
NE2 A:HIS38 4.7 10.9 0.7
NE2 A:HIS215 4.8 9.7 1.0
CD2 A:HIS63 4.8 9.1 1.0
CZ A:PHE212 4.9 9.2 1.0
NE2 A:HIS54 4.9 13.8 1.0
CZ A:PHE59 5.0 9.2 1.0

Copper binding site 4 out of 6 in 2zwg

Go back to Copper Binding Sites List in 2zwg
Copper binding site 4 out of 6 in the Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours


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 the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu504

b:37.7
occ:0.50
 NE2 A:HIS277 2.0 33.6 1.0
O A:HOH829 2.5 35.9 1.0
O A:HOH924 2.6 27.8 0.5
CE1 A:HIS277 2.8 35.7 1.0
CD2 A:HIS277 3.2 38.6 1.0
ND1 A:HIS277 4.0 37.9 1.0
CG A:HIS277 4.2 41.8 1.0
CG A:PRO231 4.7 21.9 1.0
O A:HOH839 4.7 37.0 1.0

Copper binding site 5 out of 6 in 2zwg

Go back to Copper Binding Sites List in 2zwg
Copper binding site 5 out of 6 in the Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours


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 the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu503

b:14.8
occ:0.54
 NE2 B:HIS82 2.0 17.4 0.5
NE2 B:HIS97 2.1 25.5 1.0
SD B:MET84 2.2 23.7 1.0
CE1 B:HIS82 2.3 18.1 0.5
CE1 B:HIS82 2.9 17.4 0.5
CE1 B:HIS97 2.9 24.6 1.0
CG B:MET84 2.9 21.7 1.0
CD2 B:HIS82 3.1 17.2 0.5
ND1 B:HIS82 3.1 16.9 0.5
O A:ILE42 3.2 13.7 1.0
CD2 B:HIS97 3.3 20.6 1.0
NE2 B:HIS82 3.3 16.2 0.5
CE B:MET84 3.4 18.1 1.0
CB B:MET84 3.6 12.9 1.0
CA A:MET43 3.7 15.5 1.0
ND1 B:HIS82 4.0 15.0 0.5
O A:MET43 4.0 18.4 1.0
ND1 B:HIS97 4.1 16.7 1.0
CG B:HIS82 4.2 15.2 0.5
C A:ILE42 4.2 13.1 1.0
C A:MET43 4.2 15.1 1.0
CG B:HIS97 4.3 16.4 1.0
CG B:HIS82 4.4 14.6 0.5
N A:MET43 4.4 11.7 1.0
CD2 B:HIS82 4.4 17.4 0.5
O A:HOH540 4.6 14.4 1.0
CB A:MET43 4.6 17.1 1.0
CG A:MET43 4.8 17.2 1.0
CA B:MET84 4.8 13.2 1.0
N B:MET84 4.8 11.0 1.0
CG1 B:ILE92 4.9 14.1 1.0
C B:VAL83 5.0 11.7 1.0

Copper binding site 6 out of 6 in 2zwg

Go back to Copper Binding Sites List in 2zwg
Copper binding site 6 out of 6 in the Crystal Structure of the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours


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 the Copper-Bound Tyrosinase in Complex with A Caddie Protein From Streptomyces Castaneoglobisporus Obtained By Soaking the Deoxy-Form Crystal in Dioxygen-Saturated Solution For 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu503

b:24.3
occ:0.46
 NE2 B:HIS82 3.2 16.2 0.5
CD2 B:HIS82 3.2 17.4 0.5
ND1 B:HIS82 3.7 15.0 0.5
CE1 B:HIS82 3.8 17.4 0.5
O A:MET43 4.0 18.4 1.0
CE1 B:HIS82 4.5 18.1 0.5
CG B:HIS82 4.6 14.6 0.5
O B:HOH598 4.8 19.0 1.0

Reference:

Y.Matoba, H.Yoshitsu, H.J.Jeon, K.Oda, M.Noda, T.Kumagai, M.Sugiyama. Crystallographic Evidence of Drastic Movement of A Copper Ion Toward the Substrate Tyrosine For Starting Hydroxylation Reaction of Tyrosinase To Be Published.
Page generated: Wed Jul 31 00:31:41 2024

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