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Copper in PDB 6ju9: Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine

Enzymatic activity of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine

All present enzymatic activity of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine:
1.14.18.1;

Protein crystallography data

The structure of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine, PDB code: 6ju9 was solved by N.Fujieda, K.Umakoshi, Y.Nishikawa, G.Kurisu, S.Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.544, 104.970, 154.877, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.7

Copper Binding Sites:

The binding sites of Copper atom in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine (pdb code 6ju9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine, PDB code: 6ju9:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 6ju9

Go back to Copper Binding Sites List in 6ju9
Copper binding site 1 out of 8 in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:15.8
occ:0.52
 CU A:CU503 0.0 15.8 0.5
NE2 A:HIS103 2.0 10.6 1.0
O A:HOH613 2.0 19.0 1.0
NE2 A:HIS67 2.1 13.5 1.0
CU A:CU503 2.2 17.0 0.4
NE2 A:HIS94 2.5 20.6 1.0
CE1 A:HIS103 2.8 8.7 1.0
CD2 A:HIS67 2.8 13.2 1.0
CE1 A:HIS94 3.1 19.3 1.0
CD2 A:HIS103 3.2 9.6 1.0
CE1 A:HIS67 3.3 13.2 1.0
CD2 A:HIS94 3.6 24.1 1.0
CU A:CU504 3.7 11.2 0.4
OE2 A:DAH502 3.7 21.4 0.5
CB A:ALA92 3.8 11.2 1.0
ND1 A:HIS103 4.0 9.0 1.0
CG A:HIS67 4.1 10.8 1.0
NE2 A:HIS372 4.1 10.9 1.0
CZ A:PHE368 4.1 9.9 1.0
OH A:TYR501 4.1 17.8 0.4
CU A:CU504 4.2 11.8 0.5
ND1 A:HIS94 4.2 16.5 1.0
CG A:HIS103 4.2 9.3 1.0
ND1 A:HIS67 4.3 11.1 1.0
CE2 A:PHE368 4.4 8.6 1.0
CE1 A:HIS372 4.4 9.5 1.0
OZ A:DAH502 4.4 16.6 0.5
CG A:HIS94 4.5 16.5 1.0
CZ3 A:TRP102 4.6 8.0 1.0
O A:VAL93 4.9 11.5 1.0
CE1 A:PHE99 4.9 8.9 1.0
NE2 A:HIS328 4.9 10.1 1.0
CE2 A:DAH502 4.9 18.2 0.5
CA A:ALA92 5.0 10.2 1.0

Copper binding site 2 out of 8 in 6ju9

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Copper binding site 2 out of 8 in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:17.0
occ:0.37
 CU A:CU503 0.0 17.0 0.4
O A:HOH613 1.8 19.0 1.0
OH A:TYR501 2.0 17.8 0.4
NE2 A:HIS94 2.1 20.6 1.0
OE2 A:DAH502 2.1 21.4 0.5
NE2 A:HIS67 2.2 13.5 1.0
CU A:CU503 2.2 15.8 0.5
OZ A:DAH502 2.4 16.6 0.5
CE1 A:HIS67 2.5 13.2 1.0
CE1 A:HIS94 2.6 19.3 1.0
CE2 A:DAH502 3.0 18.2 0.5
CZ A:DAH502 3.1 16.6 0.5
CZ A:TYR501 3.1 17.6 0.4
CD2 A:HIS94 3.3 24.1 1.0
CU A:CU504 3.3 11.2 0.4
CE2 A:TYR501 3.5 18.9 0.4
CD2 A:HIS67 3.6 13.2 1.0
ND1 A:HIS94 3.8 16.5 1.0
ND1 A:HIS67 3.8 11.1 1.0
CU A:CU504 3.8 11.8 0.5
NE2 A:HIS103 4.1 10.6 1.0
CG A:HIS94 4.2 16.5 1.0
CE2 A:PHE368 4.3 8.6 1.0
CD2 A:DAH502 4.3 19.0 0.5
CG A:HIS67 4.3 10.8 1.0
CE1 A:TYR501 4.4 16.9 0.4
NE2 A:HIS332 4.4 9.7 1.0
CE1 A:DAH502 4.4 15.7 0.5
CG2 A:VAL359 4.5 19.7 1.0
CG1 A:VAL359 4.5 17.4 1.0
NE2 A:HIS328 4.6 10.1 1.0
CE1 A:HIS332 4.7 11.1 1.0
CZ A:PHE368 4.7 9.9 1.0
NE2 A:HIS372 4.7 10.9 1.0
CE1 A:HIS103 4.7 8.7 1.0
CE1 A:HIS328 4.8 10.1 1.0
CD2 A:TYR501 4.8 19.2 0.4
CB A:ALA92 4.9 11.2 1.0
CB A:VAL359 4.9 11.9 1.0
CA A:VAL359 4.9 11.1 1.0

Copper binding site 3 out of 8 in 6ju9

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Copper binding site 3 out of 8 in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu504

b:11.8
occ:0.49
 CU A:CU504 0.0 11.8 0.5
CU A:CU504 0.5 11.2 0.4
NE2 A:HIS332 1.9 9.7 1.0
NE2 A:HIS372 1.9 10.9 1.0
NE2 A:HIS328 2.2 10.1 1.0
O A:HOH613 2.3 19.0 1.0
CD2 A:HIS372 2.8 9.9 1.0
CE1 A:HIS332 2.9 11.1 1.0
CD2 A:HIS328 2.9 7.7 1.0
CD2 A:HIS332 2.9 9.1 1.0
CE1 A:HIS372 2.9 9.5 1.0
CE1 A:HIS328 3.3 10.1 1.0
OE2 A:DAH502 3.5 21.4 0.5
CE2 A:PHE368 3.8 8.6 1.0
CU A:CU503 3.8 17.0 0.4
OH A:TYR501 3.9 17.8 0.4
ND1 A:HIS332 4.0 10.1 1.0
ND1 A:HIS372 4.0 8.6 1.0
CG A:HIS372 4.0 8.3 1.0
CG A:HIS332 4.0 8.1 1.0
OZ A:DAH502 4.0 16.6 0.5
CE2 A:DAH502 4.1 18.2 0.5
CG A:HIS328 4.1 9.6 1.0
CD2 A:HIS371 4.1 9.8 1.0
CU A:CU503 4.2 15.8 0.5
ND1 A:HIS328 4.3 10.1 1.0
CZ A:DAH502 4.3 16.6 0.5
CZ A:TYR501 4.3 17.6 0.4
CZ A:PHE368 4.4 9.9 1.0
CE2 A:TYR501 4.4 18.9 0.4
CD2 A:PHE368 4.4 7.8 1.0
NE2 A:HIS371 4.5 9.1 1.0
NE2 A:HIS103 4.7 10.6 1.0
CD2 A:HIS103 4.9 9.6 1.0
CD2 A:DAH502 5.0 19.0 0.5
NE2 A:HIS67 5.0 13.5 1.0

Copper binding site 4 out of 8 in 6ju9

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Copper binding site 4 out of 8 in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu504

b:11.2
occ:0.43
 CU A:CU504 0.0 11.2 0.4
CU A:CU504 0.5 11.8 0.5
O A:HOH613 1.8 19.0 1.0
NE2 A:HIS372 2.0 10.9 1.0
NE2 A:HIS332 2.1 9.7 1.0
NE2 A:HIS328 2.1 10.1 1.0
CE1 A:HIS372 3.0 9.5 1.0
CE1 A:HIS332 3.1 11.1 1.0
CD2 A:HIS328 3.1 7.7 1.0
OE2 A:DAH502 3.1 21.4 0.5
CD2 A:HIS332 3.1 9.1 1.0
CD2 A:HIS372 3.1 9.9 1.0
CE1 A:HIS328 3.1 10.1 1.0
CU A:CU503 3.3 17.0 0.4
OH A:TYR501 3.5 17.8 0.4
CU A:CU503 3.7 15.8 0.5
OZ A:DAH502 3.7 16.6 0.5
CE2 A:DAH502 3.7 18.2 0.5
CE2 A:PHE368 3.8 8.6 1.0
CZ A:DAH502 4.0 16.6 0.5
CZ A:TYR501 4.0 17.6 0.4
CE2 A:TYR501 4.1 18.9 0.4
ND1 A:HIS372 4.1 8.6 1.0
ND1 A:HIS332 4.2 10.1 1.0
CG A:HIS332 4.2 8.1 1.0
CG A:HIS372 4.2 8.3 1.0
CG A:HIS328 4.2 9.6 1.0
ND1 A:HIS328 4.2 10.1 1.0
CZ A:PHE368 4.3 9.9 1.0
NE2 A:HIS103 4.3 10.6 1.0
NE2 A:HIS94 4.5 20.6 1.0
CD2 A:PHE368 4.5 7.8 1.0
NE2 A:HIS67 4.5 13.5 1.0
CD2 A:HIS371 4.7 9.8 1.0
CD2 A:HIS103 4.7 9.6 1.0
CD2 A:DAH502 4.7 19.0 0.5
CE1 A:PHE99 4.8 8.9 1.0

Copper binding site 5 out of 8 in 6ju9

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Copper binding site 5 out of 8 in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:16.3
occ:0.58
 CU B:CU502 0.0 16.3 0.6
NE2 B:HIS103 2.0 13.5 1.0
NE2 B:HIS67 2.1 16.0 1.0
O B:HOH843 2.1 24.7 1.0
CU B:CU502 2.3 17.4 0.3
NE2 B:HIS94 2.4 21.9 1.0
CE1 B:HIS103 2.8 13.8 1.0
CD2 B:HIS67 2.8 13.2 1.0
CE1 B:HIS94 3.0 21.5 1.0
CD2 B:HIS103 3.1 12.2 1.0
CE1 B:HIS67 3.3 15.8 1.0
CD2 B:HIS94 3.5 25.5 1.0
CB B:ALA92 3.8 16.4 1.0
CU B:CU503 3.8 13.9 0.4
ND1 B:HIS103 4.0 11.2 1.0
CG B:HIS67 4.1 12.6 1.0
CZ B:PHE368 4.2 13.7 1.0
ND1 B:HIS94 4.2 19.6 1.0
CG B:HIS103 4.2 12.3 1.0
NE2 B:HIS372 4.2 13.0 1.0
CU B:CU503 4.2 12.7 0.5
ND1 B:HIS67 4.2 13.6 1.0
OH B:TYR501 4.4 17.2 0.7
CE2 B:PHE368 4.4 10.3 1.0
CG B:HIS94 4.4 21.1 1.0
CE1 B:HIS372 4.4 12.4 1.0
CZ3 B:TRP102 4.6 12.7 1.0
O B:VAL93 4.8 15.4 1.0
CE1 B:PHE99 4.9 11.5 1.0
NE2 B:HIS328 4.9 11.9 1.0
CA B:ALA92 5.0 13.2 1.0
CE3 B:TRP102 5.0 11.9 1.0

Copper binding site 6 out of 8 in 6ju9

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Copper binding site 6 out of 8 in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:17.4
occ:0.26
 CU B:CU502 0.0 17.4 0.3
O B:HOH843 1.8 24.7 1.0
NE2 B:HIS94 2.1 21.9 1.0
OH B:TYR501 2.2 17.2 0.7
CU B:CU502 2.3 16.3 0.6
NE2 B:HIS67 2.4 16.0 1.0
CE1 B:HIS67 2.5 15.8 1.0
CE1 B:HIS94 2.6 21.5 1.0
CZ B:TYR501 3.0 15.1 0.7
CE1 B:TYR501 3.1 15.1 0.7
CD2 B:HIS94 3.3 25.5 1.0
CU B:CU503 3.3 13.9 0.4
CD2 B:HIS67 3.7 13.2 1.0
ND1 B:HIS94 3.8 19.6 1.0
CU B:CU503 3.8 12.7 0.5
ND1 B:HIS67 3.9 13.6 1.0
NE2 B:HIS103 4.1 13.5 1.0
CG B:HIS94 4.2 21.1 1.0
CE2 B:PHE368 4.3 10.3 1.0
NE2 B:HIS332 4.4 11.7 1.0
CE2 B:TYR501 4.4 13.3 0.7
CG B:HIS67 4.4 12.6 1.0
CD1 B:TYR501 4.5 16.4 0.7
NE2 B:HIS328 4.5 11.9 1.0
CG1 B:VAL359 4.5 23.4 1.0
CG2 B:VAL359 4.6 20.1 1.0
CE1 B:HIS332 4.6 13.3 1.0
CE1 B:HIS328 4.7 11.8 1.0
CZ B:PHE368 4.8 13.7 1.0
NE2 B:HIS372 4.8 13.0 1.0
CE1 B:HIS103 4.8 13.8 1.0
CA B:VAL359 4.9 14.0 1.0
CB B:VAL359 4.9 17.0 1.0
CB B:ALA92 5.0 16.4 1.0

Copper binding site 7 out of 8 in 6ju9

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Copper binding site 7 out of 8 in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu503

b:12.7
occ:0.48
 CU B:CU503 0.0 12.7 0.5
CU B:CU503 0.6 13.9 0.4
NE2 B:HIS372 1.9 13.0 1.0
NE2 B:HIS332 1.9 11.7 1.0
NE2 B:HIS328 2.2 11.9 1.0
O B:HOH843 2.3 24.7 1.0
CD2 B:HIS372 2.8 11.2 1.0
CE1 B:HIS372 2.9 12.4 1.0
CE1 B:HIS332 2.9 13.3 1.0
CD2 B:HIS332 2.9 10.8 1.0
CD2 B:HIS328 2.9 11.4 1.0
CE1 B:HIS328 3.3 11.8 1.0
CE2 B:PHE368 3.7 10.3 1.0
CU B:CU502 3.8 17.4 0.3
ND1 B:HIS372 3.9 10.7 1.0
CG B:HIS372 4.0 9.5 1.0
ND1 B:HIS332 4.0 11.3 1.0
CG B:HIS332 4.1 10.7 1.0
OH B:TYR501 4.1 17.2 0.7
CG B:HIS328 4.2 11.2 1.0
CD2 B:HIS371 4.2 11.8 1.0
CE1 B:TYR501 4.2 15.1 0.7
CU B:CU502 4.2 16.3 0.6
CD2 B:PHE368 4.3 11.2 1.0
ND1 B:HIS328 4.3 12.2 1.0
CZ B:PHE368 4.3 13.7 1.0
CZ B:TYR501 4.4 15.1 0.7
NE2 B:HIS371 4.6 10.8 1.0
NE2 B:HIS103 4.7 13.5 1.0
CD2 B:HIS103 4.9 12.2 1.0
NE2 B:HIS67 5.0 16.0 1.0

Copper binding site 8 out of 8 in 6ju9

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Copper binding site 8 out of 8 in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant Complexed with L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu503

b:13.9
occ:0.42
 CU B:CU503 0.0 13.9 0.4
CU B:CU503 0.6 12.7 0.5
O B:HOH843 1.8 24.7 1.0
NE2 B:HIS328 2.0 11.9 1.0
NE2 B:HIS372 2.1 13.0 1.0
NE2 B:HIS332 2.2 11.7 1.0
CE1 B:HIS372 2.9 12.4 1.0
CD2 B:HIS328 2.9 11.4 1.0
CE1 B:HIS328 3.0 11.8 1.0
CD2 B:HIS332 3.1 10.8 1.0
CE1 B:HIS332 3.2 13.3 1.0
CD2 B:HIS372 3.2 11.2 1.0
CU B:CU502 3.3 17.4 0.3
OH B:TYR501 3.8 17.2 0.7
CU B:CU502 3.8 16.3 0.6
CE1 B:TYR501 3.8 15.1 0.7
CE2 B:PHE368 3.9 10.3 1.0
CZ B:TYR501 4.1 15.1 0.7
ND1 B:HIS328 4.1 12.2 1.0
CG B:HIS328 4.1 11.2 1.0
ND1 B:HIS372 4.1 10.7 1.0
CG B:HIS332 4.2 10.7 1.0
ND1 B:HIS332 4.2 11.3 1.0
CG B:HIS372 4.3 9.5 1.0
NE2 B:HIS103 4.4 13.5 1.0
CZ B:PHE368 4.5 13.7 1.0
NE2 B:HIS94 4.5 21.9 1.0
CD2 B:PHE368 4.6 11.2 1.0
NE2 B:HIS67 4.7 16.0 1.0
CE1 B:PHE99 4.7 11.5 1.0
CD2 B:HIS371 4.7 11.8 1.0
CD2 B:HIS103 4.7 12.2 1.0
CD1 B:TYR501 4.8 16.4 0.7

Reference:

N.Fujieda, K.Umakoshi, Y.Ochi, Y.Nishikawa, S.Yanagisawa, M.Kubo, G.Kurisu, S.Itoh. Copper-Oxygen Dynamics in Tyrosinase Mechanism. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32356371
DOI: 10.1002/ANIE.202004733
Page generated: Wed Jul 31 06:20:10 2024

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