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Copper in PDB 6ju8: Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant

Enzymatic activity of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant

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

Protein crystallography data

The structure of Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant, PDB code: 6ju8 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 / 1.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.153, 104.482, 154.382, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.7

Copper Binding Sites:

The binding sites of Copper atom in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant (pdb code 6ju8). 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, PDB code: 6ju8:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 6ju8

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Copper binding site 1 out of 8 in the Aspergillus Oryzae Active-Tyrosinase Copper-Bound C92A Mutant


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

b:14.9
occ:0.51
 CU A:CU501 0.0 14.9 0.5
O A:HOH770 1.9 22.1 1.0
NE2 A:HIS103 2.0 10.6 1.0
CU A:CU501 2.1 16.0 0.3
NE2 A:HIS67 2.1 12.7 1.0
NE2 A:HIS94 2.2 20.6 1.0
CE1 A:HIS103 2.8 9.8 1.0
CD2 A:HIS67 2.8 11.3 1.0
CE1 A:HIS94 2.9 18.4 1.0
CD2 A:HIS103 3.2 9.8 1.0
CE1 A:HIS67 3.3 12.2 1.0
CD2 A:HIS94 3.4 24.6 1.0
CU A:CU502 3.7 11.1 0.4
CB A:ALA92 3.8 12.0 1.0
ND1 A:HIS103 4.0 9.7 1.0
ND1 A:HIS94 4.0 15.7 1.0
CU A:CU502 4.1 10.9 0.5
CG A:HIS67 4.1 8.6 1.0
NE2 A:HIS372 4.2 10.3 1.0
CG A:HIS103 4.2 9.4 1.0
O A:HOH985 4.2 23.8 1.0
ND1 A:HIS67 4.3 10.1 1.0
CG A:HIS94 4.3 15.5 1.0
CZ A:PHE368 4.3 10.0 1.0
CE1 A:HIS372 4.5 9.7 1.0
CE2 A:PHE368 4.5 9.4 1.0
CZ3 A:TRP102 4.6 8.6 1.0
O A:VAL93 4.8 12.2 1.0
CE1 A:PHE99 4.8 9.8 1.0
NE2 A:HIS328 4.9 10.2 1.0
CA A:ALA92 5.0 11.1 1.0

Copper binding site 2 out of 8 in 6ju8

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


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

b:16.0
occ:0.29
 CU A:CU501 0.0 16.0 0.3
O A:HOH770 1.7 22.1 1.0
NE2 A:HIS94 2.0 20.6 1.0
CU A:CU501 2.1 14.9 0.5
NE2 A:HIS67 2.2 12.7 1.0
O A:HOH985 2.2 23.8 1.0
CE1 A:HIS94 2.5 18.4 1.0
CE1 A:HIS67 2.5 12.2 1.0
CD2 A:HIS94 3.2 24.6 1.0
CU A:CU502 3.3 11.1 0.4
CD2 A:HIS67 3.5 11.3 1.0
CU A:CU502 3.7 10.9 0.5
ND1 A:HIS94 3.7 15.7 1.0
ND1 A:HIS67 3.9 10.1 1.0
NE2 A:HIS103 4.0 10.6 1.0
CG A:HIS94 4.1 15.5 1.0
CG2 A:VAL359 4.3 20.7 1.0
CE2 A:PHE368 4.3 9.4 1.0
CG A:HIS67 4.3 8.6 1.0
CG1 A:VAL359 4.4 17.1 1.0
NE2 A:HIS332 4.4 9.4 1.0
NE2 A:HIS328 4.5 10.2 1.0
CE1 A:HIS103 4.6 9.8 1.0
CE1 A:HIS328 4.7 11.0 1.0
NE2 A:HIS372 4.7 10.3 1.0
CB A:VAL359 4.8 13.4 1.0
CE1 A:HIS332 4.8 10.2 1.0
CZ A:PHE368 4.8 10.0 1.0
CB A:ALA92 4.8 12.0 1.0
CA A:VAL359 4.9 10.2 1.0
O A:HOH949 4.9 24.0 1.0
O A:HOH975 5.0 33.1 1.0

Copper binding site 3 out of 8 in 6ju8

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


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

b:10.9
occ:0.53
 CU A:CU502 0.0 10.9 0.5
CU A:CU502 0.6 11.1 0.4
NE2 A:HIS372 1.9 10.3 1.0
NE2 A:HIS332 1.9 9.4 1.0
NE2 A:HIS328 2.2 10.2 1.0
O A:HOH770 2.3 22.1 1.0
CD2 A:HIS372 2.8 10.3 1.0
CE1 A:HIS332 2.9 10.2 1.0
CE1 A:HIS372 2.9 9.7 1.0
CD2 A:HIS332 2.9 9.4 1.0
CD2 A:HIS328 3.0 9.4 1.0
CE1 A:HIS328 3.3 11.0 1.0
CU A:CU501 3.7 16.0 0.3
CE2 A:PHE368 3.7 9.4 1.0
O A:HOH985 3.8 23.8 1.0
ND1 A:HIS372 4.0 9.6 1.0
CG A:HIS372 4.0 8.9 1.0
ND1 A:HIS332 4.0 10.5 1.0
CG A:HIS332 4.0 8.4 1.0
CU A:CU501 4.1 14.9 0.5
CG A:HIS328 4.2 9.8 1.0
CD2 A:HIS371 4.3 9.6 1.0
ND1 A:HIS328 4.3 11.1 1.0
CZ A:PHE368 4.3 10.0 1.0
CD2 A:PHE368 4.4 9.2 1.0
NE2 A:HIS103 4.6 10.6 1.0
NE2 A:HIS371 4.6 9.8 1.0
NE2 A:HIS67 4.8 12.7 1.0
CD2 A:HIS103 4.9 9.8 1.0
NE2 A:HIS94 4.9 20.6 1.0
O A:HOH975 5.0 33.1 1.0

Copper binding site 4 out of 8 in 6ju8

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


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

b:11.1
occ:0.40
 CU A:CU502 0.0 11.1 0.4
CU A:CU502 0.6 10.9 0.5
NE2 A:HIS328 1.9 10.2 1.0
O A:HOH770 1.9 22.1 1.0
NE2 A:HIS372 2.1 10.3 1.0
NE2 A:HIS332 2.2 9.4 1.0
CE1 A:HIS328 2.9 11.0 1.0
CE1 A:HIS372 2.9 9.7 1.0
CD2 A:HIS328 2.9 9.4 1.0
CD2 A:HIS332 3.1 9.4 1.0
CE1 A:HIS332 3.2 10.2 1.0
CD2 A:HIS372 3.3 10.3 1.0
CU A:CU501 3.3 16.0 0.3
O A:HOH985 3.6 23.8 1.0
CU A:CU501 3.7 14.9 0.5
ND1 A:HIS328 4.0 11.1 1.0
CE2 A:PHE368 4.0 9.4 1.0
CG A:HIS328 4.0 9.8 1.0
ND1 A:HIS372 4.1 9.6 1.0
CG A:HIS332 4.2 8.4 1.0
ND1 A:HIS332 4.3 10.5 1.0
NE2 A:HIS103 4.3 10.6 1.0
CG A:HIS372 4.3 8.9 1.0
NE2 A:HIS94 4.3 20.6 1.0
NE2 A:HIS67 4.6 12.7 1.0
CZ A:PHE368 4.6 10.0 1.0
CE1 A:PHE99 4.6 9.8 1.0
CD2 A:HIS103 4.7 9.8 1.0
O A:HOH975 4.7 33.1 1.0
CD2 A:HIS371 4.8 9.6 1.0
CD2 A:PHE368 4.8 9.2 1.0
CD2 A:HIS94 4.9 24.6 1.0
CZ A:PHE99 5.0 8.7 1.0
CE1 A:HIS103 5.0 9.8 1.0

Copper binding site 5 out of 8 in 6ju8

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


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

b:18.4
occ:0.59
 CU B:CU501 0.0 18.4 0.6
NE2 B:HIS103 2.0 16.1 1.0
O B:HOH713 2.0 26.9 1.0
NE2 B:HIS67 2.0 16.1 1.0
CU B:CU501 2.1 19.2 0.2
NE2 B:HIS94 2.2 23.6 1.0
CE1 B:HIS103 2.8 15.5 1.0
CD2 B:HIS67 2.8 15.8 1.0
CE1 B:HIS94 3.0 21.8 1.0
CE1 B:HIS67 3.2 16.7 1.0
CD2 B:HIS103 3.2 15.0 1.0
O B:HOH710 3.2 37.7 1.0
CD2 B:HIS94 3.3 26.5 1.0
CU B:CU502 3.7 14.4 0.3
CB B:ALA92 3.7 16.3 1.0
ND1 B:HIS103 4.0 15.6 1.0
ND1 B:HIS94 4.1 19.9 1.0
CG B:HIS67 4.1 14.7 1.0
CU B:CU502 4.2 14.2 0.6
ND1 B:HIS67 4.2 15.3 1.0
CG B:HIS103 4.2 14.8 1.0
NE2 B:HIS372 4.2 13.2 1.0
CG B:HIS94 4.3 21.3 1.0
O B:HOH918 4.3 28.0 1.0
CZ B:PHE368 4.3 12.4 1.0
CE1 B:HIS372 4.5 13.9 1.0
CE2 B:PHE368 4.5 12.0 1.0
CZ3 B:TRP102 4.6 14.9 1.0
O B:VAL93 4.7 19.8 1.0
CE1 B:PHE99 4.8 13.8 1.0
NE2 B:HIS328 4.9 13.5 1.0
CA B:ALA92 5.0 17.5 1.0

Copper binding site 6 out of 8 in 6ju8

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


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

b:19.2
occ:0.23
 CU B:CU501 0.0 19.2 0.2
O B:HOH713 1.7 26.9 1.0
O B:HOH710 1.8 37.7 1.0
NE2 B:HIS94 2.0 23.6 1.0
CU B:CU501 2.1 18.4 0.6
NE2 B:HIS67 2.2 16.1 1.0
O B:HOH918 2.3 28.0 1.0
CE1 B:HIS67 2.5 16.7 1.0
CE1 B:HIS94 2.6 21.8 1.0
CD2 B:HIS94 3.1 26.5 1.0
CU B:CU502 3.2 14.4 0.3
CD2 B:HIS67 3.6 15.8 1.0
CU B:CU502 3.7 14.2 0.6
ND1 B:HIS94 3.8 19.9 1.0
ND1 B:HIS67 3.8 15.3 1.0
NE2 B:HIS103 4.0 16.1 1.0
CG B:HIS94 4.0 21.3 1.0
CE2 B:PHE368 4.3 12.0 1.0
CG B:HIS67 4.4 14.7 1.0
CG1 B:VAL359 4.4 29.9 1.0
NE2 B:HIS332 4.5 12.7 1.0
NE2 B:HIS328 4.6 13.5 1.0
CG2 B:VAL359 4.6 23.8 1.0
CE1 B:HIS103 4.6 15.5 1.0
NE2 B:HIS372 4.7 13.2 1.0
CE1 B:HIS328 4.7 14.9 1.0
CZ B:PHE368 4.8 12.4 1.0
CE1 B:HIS332 4.8 14.0 1.0
CB B:ALA92 4.8 16.3 1.0
CB B:VAL359 4.9 17.6 1.0

Copper binding site 7 out of 8 in 6ju8

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


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

b:14.2
occ:0.60
 CU B:CU502 0.0 14.2 0.6
CU B:CU502 0.7 14.4 0.3
NE2 B:HIS372 1.9 13.2 1.0
NE2 B:HIS332 1.9 12.7 1.0
NE2 B:HIS328 2.2 13.5 1.0
O B:HOH713 2.3 26.9 1.0
O B:HOH710 2.9 37.7 1.0
CD2 B:HIS372 2.9 13.3 1.0
CE1 B:HIS332 2.9 14.0 1.0
CE1 B:HIS372 2.9 13.9 1.0
CD2 B:HIS332 2.9 12.2 1.0
CD2 B:HIS328 3.0 11.9 1.0
CE1 B:HIS328 3.3 14.9 1.0
CU B:CU501 3.7 19.2 0.2
CE2 B:PHE368 3.8 12.0 1.0
O B:HOH918 3.8 28.0 1.0
CG B:HIS372 4.0 11.7 1.0
ND1 B:HIS372 4.0 12.3 1.0
ND1 B:HIS332 4.0 12.2 1.0
CG B:HIS332 4.1 11.3 1.0
CU B:CU501 4.2 18.4 0.6
CG B:HIS328 4.2 12.4 1.0
CD2 B:HIS371 4.3 12.2 1.0
CZ B:PHE368 4.3 12.4 1.0
ND1 B:HIS328 4.3 14.3 1.0
CD2 B:PHE368 4.4 12.2 1.0
NE2 B:HIS371 4.7 12.6 1.0
NE2 B:HIS103 4.7 16.1 1.0
NE2 B:HIS67 4.9 16.1 1.0
CD2 B:HIS103 4.9 15.0 1.0
NE2 B:HIS94 5.0 23.6 1.0

Copper binding site 8 out of 8 in 6ju8

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


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

b:14.4
occ:0.30
 CU B:CU502 0.0 14.4 0.3
CU B:CU502 0.7 14.2 0.6
O B:HOH713 1.9 26.9 1.0
NE2 B:HIS328 1.9 13.5 1.0
NE2 B:HIS372 2.2 13.2 1.0
O B:HOH710 2.3 37.7 1.0
NE2 B:HIS332 2.3 12.7 1.0
CE1 B:HIS328 2.9 14.9 1.0
CE1 B:HIS372 3.0 13.9 1.0
CD2 B:HIS328 3.0 11.9 1.0
CD2 B:HIS332 3.2 12.2 1.0
CU B:CU501 3.2 19.2 0.2
CE1 B:HIS332 3.3 14.0 1.0
CD2 B:HIS372 3.3 13.3 1.0
O B:HOH918 3.5 28.0 1.0
CU B:CU501 3.7 18.4 0.6
ND1 B:HIS328 4.0 14.3 1.0
CE2 B:PHE368 4.1 12.0 1.0
CG B:HIS328 4.1 12.4 1.0
ND1 B:HIS372 4.2 12.3 1.0
NE2 B:HIS103 4.3 16.1 1.0
CG B:HIS332 4.3 11.3 1.0
NE2 B:HIS94 4.4 23.6 1.0
CG B:HIS372 4.4 11.7 1.0
ND1 B:HIS332 4.4 12.2 1.0
CE1 B:PHE99 4.5 13.8 1.0
NE2 B:HIS67 4.6 16.1 1.0
CZ B:PHE368 4.6 12.4 1.0
CD2 B:HIS103 4.7 15.0 1.0
CD2 B:HIS94 4.8 26.5 1.0
CD2 B:PHE368 4.9 12.2 1.0
CD2 B:HIS371 4.9 12.2 1.0
CZ B:PHE99 4.9 14.5 1.0
CE1 B:HIS67 5.0 16.7 1.0
CE1 B:HIS103 5.0 15.5 1.0

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 06:19:42 2024

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