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Copper in PDB 2zwf: 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 80 Minutes

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 80 Minutes

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 80 Minutes:
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 80 Minutes, PDB code: 2zwf 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 / 1.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.160, 97.680, 54.990, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.2

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 80 Minutes (pdb code 2zwf). 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 80 Minutes, PDB code: 2zwf:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2zwf

Go back to Copper Binding Sites List in 2zwf
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 80 Minutes


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 80 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:19.2
occ:0.63
 CU A:CU501 0.0 19.2 0.6
CU A:CU501 1.8 16.1 0.4
O B:HOH547 2.0 15.8 1.0
O B:HOH582 2.0 19.2 1.0
NE2 A:HIS38 2.0 13.8 0.6
NE2 A:HIS54 2.1 19.8 1.0
NE2 A:HIS63 2.6 11.3 1.0
NE2 A:HIS38 2.6 13.5 0.4
CE1 A:HIS38 2.9 13.6 0.6
CD2 A:HIS54 2.9 18.9 1.0
CD2 A:HIS38 3.1 11.9 0.4
CD2 A:HIS38 3.1 11.7 0.6
CE1 A:HIS54 3.1 14.6 1.0
OE2 B:DAH98 3.2 14.9 0.4
CE1 A:HIS63 3.2 9.3 1.0
CU A:CU502 3.5 18.0 1.0
OZ B:DAH98 3.7 15.5 1.0
CD2 A:HIS63 3.7 10.7 1.0
CE1 A:HIS38 3.8 12.9 0.4
ND1 A:HIS38 4.0 12.7 0.6
CG A:HIS54 4.1 14.3 1.0
NE2 A:HIS216 4.1 10.6 1.0
ND1 A:HIS54 4.2 14.7 1.0
CG A:HIS38 4.2 11.5 0.6
CE2 A:PHE212 4.3 11.6 1.0
CZ A:PHE212 4.4 10.4 1.0
CG A:HIS38 4.4 11.0 0.4
CE2 B:DAH98 4.4 12.9 1.0
CE1 A:HIS216 4.4 11.5 1.0
ND1 A:HIS63 4.4 9.2 1.0
CZ B:DAH98 4.6 15.5 1.0
CD1 A:ILE42 4.6 25.1 1.0
NE2 A:HIS190 4.7 8.9 1.0
ND1 A:HIS38 4.7 12.5 0.4
CG A:HIS63 4.7 8.9 1.0
CE1 A:PHE59 4.9 7.5 1.0
NE2 A:HIS194 4.9 8.1 1.0

Copper binding site 2 out of 6 in 2zwf

Go back to Copper Binding Sites List in 2zwf
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 80 Minutes


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 80 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:16.1
occ:0.37
 CU A:CU501 0.0 16.1 0.4
CU A:CU501 1.8 19.2 0.6
O B:HOH547 2.1 15.8 1.0
OZ B:DAH98 2.1 15.5 1.0
NE2 A:HIS38 2.1 13.5 0.4
OE2 B:DAH98 2.1 14.9 0.4
CE1 A:HIS38 2.3 13.6 0.6
NE2 A:HIS38 2.4 13.8 0.6
NE2 A:HIS54 2.6 19.8 1.0
O B:HOH582 2.6 19.2 1.0
CE1 A:HIS38 2.9 12.9 0.4
CZ B:DAH98 3.0 15.5 1.0
CE2 B:DAH98 3.1 12.9 1.0
CD1 A:ILE42 3.2 25.1 1.0
CD2 A:HIS54 3.3 18.9 1.0
CD2 A:HIS38 3.3 11.9 0.4
ND1 A:HIS38 3.6 12.7 0.6
CE1 A:HIS54 3.6 14.6 1.0
CU A:CU502 3.7 18.0 1.0
CD2 A:HIS38 3.8 11.7 0.6
CG1 A:ILE42 4.1 25.9 1.0
ND1 A:HIS38 4.1 12.5 0.4
OG A:SER206 4.2 9.4 1.0
CG A:HIS38 4.3 11.5 0.6
CG A:HIS38 4.3 11.0 0.4
CE1 B:DAH98 4.4 11.4 1.0
NE2 A:HIS63 4.4 11.3 1.0
CD2 B:DAH98 4.4 10.2 1.0
CG A:HIS54 4.4 14.3 1.0
NE2 A:HIS194 4.5 8.1 1.0
O B:HOH556 4.5 16.4 1.0
CE1 A:HIS194 4.6 9.9 1.0
CE2 A:PHE212 4.6 11.6 1.0
ND1 A:HIS54 4.6 14.7 1.0
CB A:ILE42 4.8 19.3 1.0
CE1 A:HIS63 4.9 9.3 1.0
NE2 A:HIS190 5.0 8.9 1.0

Copper binding site 3 out of 6 in 2zwf

Go back to Copper Binding Sites List in 2zwf
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 80 Minutes


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 80 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:18.0
occ:1.00
 NE2 A:HIS194 2.0 8.1 1.0
O B:HOH547 2.0 15.8 1.0
NE2 A:HIS190 2.0 8.9 1.0
NE2 A:HIS216 2.1 10.6 1.0
O B:HOH582 2.5 19.2 1.0
CE1 A:HIS216 2.9 11.5 1.0
CE1 A:HIS194 2.9 9.9 1.0
CE1 A:HIS190 2.9 10.2 1.0
CD2 A:HIS190 3.0 8.3 1.0
CD2 A:HIS194 3.0 10.2 1.0
OE2 B:DAH98 3.2 14.9 0.4
CD2 A:HIS216 3.2 10.0 1.0
CU A:CU501 3.5 19.2 0.6
CU A:CU501 3.7 16.1 0.4
CE2 B:DAH98 3.8 12.9 1.0
OZ B:DAH98 4.0 15.5 1.0
ND1 A:HIS190 4.1 9.2 1.0
ND1 A:HIS194 4.1 9.8 1.0
ND1 A:HIS216 4.1 9.9 1.0
CG A:HIS190 4.1 8.5 1.0
CG A:HIS194 4.1 10.6 1.0
CE2 A:PHE212 4.2 11.6 1.0
CG A:HIS216 4.2 8.7 1.0
CZ B:DAH98 4.3 15.5 1.0
CD2 A:HIS215 4.5 11.3 1.0
NE2 A:HIS63 4.5 11.3 1.0
NE2 A:HIS215 4.6 10.7 1.0
CD2 B:DAH98 4.6 10.2 1.0
CZ A:PHE212 4.8 10.4 1.0
CE1 A:PHE59 4.8 7.5 1.0
CD2 A:PHE212 4.9 8.9 1.0
NE2 A:HIS38 4.9 13.8 0.6
CD2 A:HIS63 5.0 10.7 1.0

Copper binding site 4 out of 6 in 2zwf

Go back to Copper Binding Sites List in 2zwf
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 80 Minutes


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 80 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu504

b:45.4
occ:0.50
 NE2 A:HIS277 2.0 52.1 1.0
O A:HOH926 2.4 24.3 0.5
CE1 A:HIS277 2.8 51.9 1.0
O A:HOH888 2.9 44.6 1.0
CD2 A:HIS277 3.1 54.7 1.0
ND1 A:HIS277 4.0 53.9 1.0
CG A:HIS277 4.1 57.6 1.0
CG A:PRO231 4.6 22.4 1.0
O A:HOH733 4.8 30.8 1.0

Copper binding site 5 out of 6 in 2zwf

Go back to Copper Binding Sites List in 2zwf
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 80 Minutes


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 80 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu503

b:17.9
occ:0.66
 NE2 B:HIS82 2.0 13.4 0.7
NE2 B:HIS97 2.1 24.3 1.0
SD B:MET84 2.3 24.3 1.0
CE1 B:HIS82 2.8 15.5 0.3
CE1 B:HIS97 2.9 23.7 1.0
CE1 B:HIS82 2.9 15.4 0.7
CD2 B:HIS82 3.1 15.9 0.7
CG B:MET84 3.1 21.3 1.0
ND1 B:HIS82 3.2 14.6 0.3
O A:ILE42 3.2 16.1 1.0
CD2 B:HIS97 3.2 21.3 1.0
CE B:MET84 3.5 30.9 1.0
CB B:MET84 3.7 13.5 1.0
CA A:MET43 3.7 17.1 1.0
NE2 B:HIS82 4.0 15.5 0.3
ND1 B:HIS82 4.0 13.9 0.7
ND1 B:HIS97 4.1 18.3 1.0
O A:MET43 4.1 21.4 1.0
C A:ILE42 4.1 13.9 1.0
CG B:HIS82 4.2 12.8 0.7
C A:MET43 4.2 18.7 1.0
CG B:HIS97 4.3 17.0 1.0
N A:MET43 4.4 12.6 1.0
CG B:HIS82 4.5 13.0 0.3
O A:HOH576 4.6 18.4 1.0
CB A:MET43 4.7 17.6 1.0
CG A:MET43 4.8 19.8 1.0
CA B:MET84 4.8 13.7 1.0
CD1 B:ILE92 4.8 36.7 1.0
N B:MET84 4.9 12.2 1.0
CD2 B:HIS82 4.9 15.4 0.3
CG1 B:ILE92 5.0 14.9 1.0

Copper binding site 6 out of 6 in 2zwf

Go back to Copper Binding Sites List in 2zwf
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 80 Minutes


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 80 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu503

b:24.5
occ:0.34
 NE2 B:HIS82 2.6 15.5 0.3
CD2 B:HIS82 3.1 15.4 0.3
ND1 B:HIS82 3.7 13.9 0.7
CE1 B:HIS82 3.7 15.4 0.7
CE1 B:HIS82 3.8 15.5 0.3
O A:MET43 3.9 21.4 1.0
CG B:HIS82 4.4 13.0 0.3
O B:HOH586 4.7 19.0 1.0
ND1 B:HIS82 4.7 14.6 0.3
CG B:HIS82 5.0 12.8 0.7

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 00:31:37 2024

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