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Copper in PDB 2zwd: 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 5 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 5 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 5 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 5 Minutes, PDB code: 2zwd 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 / 1.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 65.200, 97.830, 55.100, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.7

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

Copper binding site 1 out of 6 in 2zwd

Go back to Copper Binding Sites List in 2zwd
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 5 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 5 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:19.1
occ:0.68
 CU A:CU1502 0.0 19.1 0.7
NE2 A:HIS38 1.8 13.9 0.7
NE2 A:HIS63 2.0 9.3 1.0
NE2 A:HIS54 2.1 21.6 1.0
NE2 A:HIS38 2.4 14.6 0.3
O B:HOH545 2.5 14.8 1.0
CD2 A:HIS38 2.7 13.0 0.3
CU A:CU1502 2.7 15.7 0.3
CE1 A:HIS63 2.7 11.3 1.0
CD2 A:HIS38 2.8 13.9 0.7
CE1 A:HIS38 2.9 14.5 0.7
CE1 A:HIS54 3.0 14.6 1.0
CD2 A:HIS54 3.2 21.4 1.0
CD2 A:HIS63 3.2 9.4 1.0
CE1 A:HIS38 3.7 13.9 0.3
CG A:HIS38 3.9 11.4 0.7
ND1 A:HIS38 3.9 12.6 0.7
ND1 A:HIS63 3.9 9.3 1.0
CG A:HIS38 4.0 11.6 0.3
CZ A:PHE212 4.1 9.4 1.0
ND1 A:HIS54 4.1 15.9 1.0
CG A:HIS54 4.2 16.5 1.0
CG A:HIS63 4.2 8.6 1.0
CE2 A:PHE212 4.3 8.8 1.0
NE2 A:HIS216 4.3 9.6 1.0
CU A:CU1503 4.3 15.1 1.0
CE1 A:HIS216 4.5 10.5 1.0
ND1 A:HIS38 4.5 11.7 0.3
CZ3 A:TRP62 4.5 9.7 1.0
OH B:TYR98 4.6 14.5 1.0
CD1 A:ILE42 4.9 32.4 1.0
O A:GLY53 4.9 10.8 1.0
CG1 A:ILE42 4.9 26.1 1.0

Copper binding site 2 out of 6 in 2zwd

Go back to Copper Binding Sites List in 2zwd
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 5 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 5 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:15.7
occ:0.32
 CU A:CU1502 0.0 15.7 0.3
O B:HOH545 1.9 14.8 1.0
OH B:TYR98 2.1 14.5 1.0
NE2 A:HIS38 2.3 14.6 0.3
CE1 A:HIS38 2.4 14.5 0.7
CU A:CU1502 2.7 19.1 0.7
CE1 A:HIS38 2.8 13.9 0.3
NE2 A:HIS38 2.8 13.9 0.7
NE2 A:HIS54 2.8 21.6 1.0
CD1 A:ILE42 3.0 32.4 1.0
CZ B:TYR98 3.1 14.4 1.0
CE2 B:TYR98 3.3 14.3 1.0
CD2 A:HIS54 3.4 21.4 1.0
CG1 A:ILE42 3.6 26.1 1.0
CD2 A:HIS38 3.6 13.0 0.3
ND1 A:HIS38 3.7 12.6 0.7
CE1 A:HIS54 3.8 14.6 1.0
CU A:CU1503 4.0 15.1 1.0
ND1 A:HIS38 4.0 11.7 0.3
OG A:SER206 4.1 10.3 1.0
CD2 A:HIS38 4.1 13.9 0.7
O B:HOH796 4.3 31.6 1.0
CE1 B:TYR98 4.3 11.1 1.0
CG A:HIS54 4.4 16.5 1.0
CG A:HIS38 4.5 11.6 0.3
NE2 A:HIS194 4.5 9.4 1.0
NE2 A:HIS63 4.6 9.3 1.0
CG A:HIS38 4.6 11.4 0.7
ND1 A:HIS54 4.6 15.9 1.0
CE1 A:HIS194 4.6 9.5 1.0
CD2 B:TYR98 4.6 12.9 1.0
CE2 A:PHE212 4.6 8.8 1.0
CE1 A:HIS190 5.0 8.8 1.0

Copper binding site 3 out of 6 in 2zwd

Go back to Copper Binding Sites List in 2zwd
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 5 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 5 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:15.1
occ:1.00
 NE2 A:HIS194 2.0 9.4 1.0
NE2 A:HIS216 2.0 9.6 1.0
NE2 A:HIS190 2.0 8.5 1.0
O B:HOH545 2.2 14.8 1.0
CE1 A:HIS216 2.9 10.5 1.0
CE1 A:HIS194 2.9 9.5 1.0
CE1 A:HIS190 3.0 8.8 1.0
CD2 A:HIS190 3.0 8.6 1.0
CD2 A:HIS194 3.0 9.5 1.0
CD2 A:HIS216 3.0 9.0 1.0
CE2 A:PHE212 4.0 8.8 1.0
CU A:CU1502 4.0 15.7 0.3
ND1 A:HIS216 4.0 9.6 1.0
ND1 A:HIS194 4.0 10.4 1.0
CG A:HIS216 4.1 8.1 1.0
ND1 A:HIS190 4.1 9.0 1.0
OH B:TYR98 4.1 14.5 1.0
CD2 A:HIS215 4.1 10.9 1.0
CG A:HIS194 4.1 8.6 1.0
CG A:HIS190 4.1 8.4 1.0
CE2 B:TYR98 4.2 14.3 1.0
NE2 A:HIS215 4.3 11.8 1.0
CU A:CU1502 4.3 19.1 0.7
CZ B:TYR98 4.4 14.4 1.0
CD2 A:PHE212 4.6 7.1 1.0
CZ A:PHE212 4.7 9.4 1.0
NE2 A:HIS63 4.8 9.3 1.0

Copper binding site 4 out of 6 in 2zwd

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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 5 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 5 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu504

b:39.5
occ:0.50
 O A:HOH819 2.1 32.5 1.0
O A:HOH969 2.3 30.1 0.5
CG A:PRO231 4.5 22.2 1.0

Copper binding site 5 out of 6 in 2zwd

Go back to Copper Binding Sites List in 2zwd
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 5 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 5 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:30.5
occ:0.47
 NE2 B:HIS82 2.7 18.8 0.5
CD2 B:HIS82 3.2 19.5 0.5
ND1 B:HIS82 3.6 16.9 0.5
CE1 B:HIS82 3.7 17.4 0.5
CE1 B:HIS82 3.8 17.7 0.5
O A:MET43 4.0 26.1 1.0
CG B:HIS82 4.4 16.7 0.5
CE B:MET84 4.5 21.4 0.5
ND1 B:HIS82 4.7 16.6 0.5
O B:HOH592 4.8 18.6 1.0
CG B:HIS82 4.9 15.9 0.5
O B:VAL83 4.9 14.5 1.0

Copper binding site 6 out of 6 in 2zwd

Go back to Copper Binding Sites List in 2zwd
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 5 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 5 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:16.0
occ:0.53
 O1 B:NO3505 1.3 18.9 0.5
NE2 B:HIS82 1.9 16.8 0.5
N B:NO3505 2.0 18.5 0.5
SD B:MET84 2.1 17.6 0.5
O2 B:NO3505 2.1 19.9 0.5
NE2 B:HIS97 2.2 19.8 0.5
CE B:MET84 2.5 16.6 0.5
CE1 B:HIS82 2.6 17.7 0.5
CE1 B:HIS82 2.7 17.4 0.5
CG B:MET84 2.7 18.8 0.5
CE1 B:HIS97 3.0 17.6 0.5
CD2 B:HIS82 3.1 15.6 0.5
O3 B:NO3505 3.1 29.5 0.5
ND1 B:HIS82 3.1 16.6 0.5
O A:ILE42 3.3 15.0 1.0
CE B:MET84 3.3 21.4 0.5
CD2 B:HIS97 3.3 18.0 0.5
SD B:MET84 3.4 19.6 0.5
CB B:MET84 3.5 16.4 1.0
CA A:MET43 3.7 15.2 1.0
CE1 B:HIS97 3.7 16.9 0.5
NE2 B:HIS82 3.7 18.8 0.5
ND1 B:HIS82 3.8 16.9 0.5
ND1 B:HIS97 4.0 15.1 0.5
CG B:MET84 4.1 21.7 0.5
CG B:HIS82 4.1 15.9 0.5
C A:ILE42 4.1 16.7 1.0
O A:MET43 4.2 26.1 1.0
ND1 B:HIS97 4.2 14.6 0.5
C A:MET43 4.2 17.6 1.0
N A:MET43 4.3 14.9 1.0
CG B:HIS97 4.4 15.0 0.5
CG B:HIS82 4.4 16.7 0.5
CB A:MET43 4.6 16.0 1.0
CG A:MET43 4.6 18.5 1.0
CD2 B:HIS82 4.7 19.5 0.5
CA B:MET84 4.7 13.7 1.0
O A:HOH554 4.8 15.9 1.0
N B:MET84 4.8 12.8 1.0
CG2 A:ILE42 4.8 24.9 1.0
C B:VAL83 4.9 11.4 1.0
O B:VAL83 4.9 14.5 1.0
NE2 B:HIS97 4.9 16.1 0.5

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 00:31:12 2024

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