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Copper in PDB 6ju5: Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y Mutant

Enzymatic activity of Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y Mutant

All present enzymatic activity of Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y Mutant:
1.14.18.1;

Protein crystallography data

The structure of Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y Mutant, PDB code: 6ju5 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 / 1.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.344, 118.210, 79.363, 90.00, 91.13, 90.00
R / Rfree (%) 15.9 / 20.2

Copper Binding Sites:

The binding sites of Copper atom in the Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y Mutant (pdb code 6ju5). 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 Pro-Tyrosinase C92A/F513Y Mutant, PDB code: 6ju5:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 6ju5

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Copper binding site 1 out of 8 in the Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y 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 Pro-Tyrosinase C92A/F513Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:15.5
occ:0.53
CU A:CU701 0.0 15.5 0.5
NE2 A:HIS103 2.0 11.8 1.0
NE2 A:HIS67 2.0 16.5 1.0
NE2 A:HIS94 2.3 19.2 1.0
CU A:CU701 2.6 18.0 0.3
O A:HOH802 2.6 26.1 1.0
CD2 A:HIS67 2.8 15.4 1.0
CE1 A:HIS103 2.8 11.2 1.0
CE1 A:HIS94 3.1 20.5 1.0
CD2 A:HIS103 3.1 10.6 1.0
CE1 A:HIS67 3.2 14.0 1.0
CD2 A:HIS94 3.3 25.9 1.0
OE2 A:DAH513 3.7 16.4 0.5
CB A:ALA92 3.7 18.1 1.0
ND1 A:HIS103 4.0 11.1 1.0
CU A:CU702 4.0 13.2 0.4
CG A:HIS67 4.0 12.3 1.0
ND1 A:HIS67 4.2 13.2 1.0
CG A:HIS103 4.2 9.9 1.0
ND1 A:HIS94 4.2 21.9 1.0
NE2 A:HIS372 4.3 10.9 1.0
CG A:HIS94 4.4 21.0 1.0
CZ A:PHE368 4.4 12.3 1.0
CE1 A:HIS372 4.4 11.1 1.0
CZ3 A:TRP102 4.5 10.3 1.0
CU A:CU702 4.5 11.7 0.5
OH A:DAH513 4.6 18.4 0.5
CE2 A:PHE368 4.7 10.6 1.0
O A:VAL93 4.8 15.2 1.0
CA A:ALA92 4.9 14.1 1.0
CE1 A:PHE99 4.9 10.1 1.0
CE3 A:TRP102 4.9 10.5 1.0
NE2 A:HIS328 5.0 10.6 1.0
CE2 A:DAH513 5.0 13.6 0.5
OZ A:DAH513 5.0 17.6 0.5

Copper binding site 2 out of 8 in 6ju5

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Copper binding site 2 out of 8 in the Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y 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 Pro-Tyrosinase C92A/F513Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:18.0
occ:0.30
CU A:CU701 0.0 18.0 0.3
OE2 A:DAH513 1.7 16.4 0.5
O A:HOH802 1.9 26.1 1.0
NE2 A:HIS94 2.2 19.2 1.0
OH A:DAH513 2.3 18.4 0.5
CE1 A:HIS67 2.5 14.0 1.0
NE2 A:HIS67 2.5 16.5 1.0
CU A:CU701 2.6 15.5 0.5
OZ A:DAH513 2.7 17.6 0.5
CE2 A:DAH513 2.7 13.6 0.5
CE2 A:DAH513 2.7 14.5 0.5
CE1 A:HIS94 2.7 20.5 1.0
CZ A:DAH513 2.9 14.8 0.5
CZ A:DAH513 3.1 14.2 0.5
CD2 A:HIS94 3.3 25.9 1.0
CU A:CU702 3.6 13.2 0.4
ND1 A:HIS67 3.8 13.2 1.0
ND1 A:HIS94 3.8 21.9 1.0
CD2 A:HIS67 3.9 15.4 1.0
CD2 A:DAH513 3.9 13.3 0.5
CD2 A:DAH513 4.0 12.7 0.5
CU A:CU702 4.1 11.7 0.5
CG A:HIS94 4.1 21.0 1.0
CG1 A:VAL359 4.2 25.1 1.0
CE1 A:DAH513 4.3 14.4 0.5
NE2 A:HIS103 4.4 11.8 1.0
CE1 A:DAH513 4.4 14.0 0.5
CG A:HIS67 4.5 12.3 1.0
NE2 A:HIS332 4.5 11.8 1.0
CG2 A:VAL359 4.5 21.8 1.0
CE2 A:PHE368 4.6 10.6 1.0
NE2 A:HIS328 4.6 10.6 1.0
CE1 A:HIS328 4.6 11.9 1.0
CE1 A:HIS332 4.7 11.7 1.0
CB A:VAL359 4.8 17.1 1.0
CA A:VAL359 4.8 15.2 1.0
NE2 A:HIS372 5.0 10.9 1.0

Copper binding site 3 out of 8 in 6ju5

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Copper binding site 3 out of 8 in the Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y 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 Pro-Tyrosinase C92A/F513Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:11.7
occ:0.52
CU A:CU702 0.0 11.7 0.5
CU A:CU702 0.7 13.2 0.4
NE2 A:HIS332 1.9 11.8 1.0
NE2 A:HIS372 1.9 10.9 1.0
NE2 A:HIS328 2.3 10.6 1.0
O A:HOH802 2.3 26.1 1.0
CE1 A:HIS332 2.8 11.7 1.0
CD2 A:HIS372 2.8 11.6 1.0
CD2 A:HIS332 3.0 10.2 1.0
CE1 A:HIS372 3.0 11.1 1.0
CD2 A:HIS328 3.0 10.6 1.0
CE1 A:HIS328 3.4 11.9 1.0
CE2 A:PHE368 3.6 10.6 1.0
OE2 A:DAH513 3.8 16.4 0.5
ND1 A:HIS332 3.9 11.1 1.0
CD2 A:HIS371 4.0 10.2 1.0
CG A:HIS372 4.0 9.3 1.0
ND1 A:HIS372 4.0 10.2 1.0
OH A:DAH513 4.0 18.4 0.5
CG A:HIS332 4.1 10.6 1.0
CU A:CU701 4.1 18.0 0.3
OZ A:DAH513 4.2 17.6 0.5
CD2 A:PHE368 4.2 10.7 1.0
CG A:HIS328 4.2 10.7 1.0
CZ A:PHE368 4.3 12.3 1.0
ND1 A:HIS328 4.3 11.0 1.0
CE2 A:DAH513 4.4 14.5 0.5
NE2 A:HIS371 4.4 10.3 1.0
CZ A:DAH513 4.5 14.8 0.5
CZ A:DAH513 4.5 14.2 0.5
CU A:CU701 4.5 15.5 0.5
CE2 A:DAH513 4.6 13.6 0.5

Copper binding site 4 out of 8 in 6ju5

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Copper binding site 4 out of 8 in the Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y 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 Pro-Tyrosinase C92A/F513Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:13.2
occ:0.42
CU A:CU702 0.0 13.2 0.4
CU A:CU702 0.7 11.7 0.5
O A:HOH802 1.8 26.1 1.0
NE2 A:HIS328 1.9 10.6 1.0
NE2 A:HIS372 2.1 10.9 1.0
NE2 A:HIS332 2.2 11.8 1.0
CE1 A:HIS328 2.9 11.9 1.0
CE1 A:HIS372 2.9 11.1 1.0
CD2 A:HIS328 2.9 10.6 1.0
CD2 A:HIS332 3.1 10.2 1.0
CE1 A:HIS332 3.1 11.7 1.0
OE2 A:DAH513 3.2 16.4 0.5
CD2 A:HIS372 3.2 11.6 1.0
CU A:CU701 3.6 18.0 0.3
OH A:DAH513 3.8 18.4 0.5
CE2 A:PHE368 3.9 10.6 1.0
CE2 A:DAH513 3.9 14.5 0.5
ND1 A:HIS328 4.0 11.0 1.0
OZ A:DAH513 4.0 17.6 0.5
CG A:HIS328 4.0 10.7 1.0
CU A:CU701 4.0 15.5 0.5
ND1 A:HIS372 4.1 10.2 1.0
CE2 A:DAH513 4.1 13.6 0.5
CZ A:DAH513 4.2 14.8 0.5
ND1 A:HIS332 4.2 11.1 1.0
CG A:HIS372 4.3 9.3 1.0
CZ A:DAH513 4.3 14.2 0.5
CG A:HIS332 4.3 10.6 1.0
CZ A:PHE368 4.5 12.3 1.0
CD2 A:HIS371 4.5 10.2 1.0
CD2 A:PHE368 4.6 10.7 1.0
NE2 A:HIS103 4.6 11.8 1.0
NE2 A:HIS67 4.7 16.5 1.0
NE2 A:HIS371 4.8 10.3 1.0
NE2 A:HIS94 4.8 19.2 1.0
CD2 A:DAH513 4.8 13.3 0.5
CE1 A:PHE99 4.9 10.1 1.0
CD2 A:HIS103 4.9 10.6 1.0

Copper binding site 5 out of 8 in 6ju5

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Copper binding site 5 out of 8 in the Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y 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 Pro-Tyrosinase C92A/F513Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:16.8
occ:0.52
CU B:CU701 0.0 16.8 0.5
NE2 B:HIS103 2.0 12.3 1.0
NE2 B:HIS67 2.0 15.9 1.0
NE2 B:HIS94 2.3 19.0 1.0
CU B:CU701 2.6 17.6 0.3
O B:HOH847 2.7 23.1 1.0
CE1 B:HIS103 2.8 12.7 1.0
CD2 B:HIS67 2.8 15.5 1.0
CE1 B:HIS67 3.1 13.9 1.0
CE1 B:HIS94 3.1 20.1 1.0
CD2 B:HIS103 3.1 11.8 1.0
CD2 B:HIS94 3.4 23.9 1.0
CB B:ALA92 3.7 15.3 1.0
OE2 B:DAH513 4.0 16.5 0.6
ND1 B:HIS103 4.0 11.6 1.0
CU B:CU702 4.0 13.5 0.4
CG B:HIS67 4.1 12.3 1.0
ND1 B:HIS67 4.2 13.3 1.0
CG B:HIS103 4.2 11.6 1.0
ND1 B:HIS94 4.3 19.0 1.0
CZ B:PHE368 4.3 11.9 1.0
NE2 B:HIS372 4.4 11.2 1.0
CG B:HIS94 4.4 18.7 1.0
CE1 B:HIS372 4.5 10.2 1.0
CZ3 B:TRP102 4.5 10.9 1.0
CU B:CU702 4.5 12.5 0.5
CE2 B:PHE368 4.6 10.1 1.0
O B:VAL93 4.7 14.6 1.0
OZ B:DAH513 4.8 15.8 0.6
OH B:DAH513 4.8 16.3 0.4
CE1 B:PHE99 4.9 10.7 1.0
CA B:ALA92 4.9 12.9 1.0
CE3 B:TRP102 4.9 10.2 1.0
NE2 B:HIS328 5.0 11.0 1.0

Copper binding site 6 out of 8 in 6ju5

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Copper binding site 6 out of 8 in the Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y 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 Pro-Tyrosinase C92A/F513Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:17.6
occ:0.26
CU B:CU701 0.0 17.6 0.3
O B:HOH847 1.9 23.1 1.0
OE2 B:DAH513 2.1 16.5 0.6
NE2 B:HIS94 2.3 19.0 1.0
OZ B:DAH513 2.4 15.8 0.6
CE1 B:HIS67 2.4 13.9 1.0
OH B:DAH513 2.5 16.3 0.4
NE2 B:HIS67 2.5 15.9 1.0
CU B:CU701 2.6 16.8 0.5
CE1 B:HIS94 2.7 20.1 1.0
CE2 B:DAH513 2.8 14.0 0.4
CE2 B:DAH513 2.9 14.1 0.6
CZ B:DAH513 3.0 12.9 0.4
CZ B:DAH513 3.1 12.2 0.6
CD2 B:HIS94 3.3 23.9 1.0
CU B:CU702 3.6 13.5 0.4
ND1 B:HIS67 3.8 13.3 1.0
ND1 B:HIS94 3.8 19.0 1.0
CD2 B:HIS67 3.9 15.5 1.0
CG1 B:VAL359 3.9 34.0 1.0
CD2 B:DAH513 4.1 13.4 0.4
CU B:CU702 4.1 12.5 0.5
CG B:HIS94 4.2 18.7 1.0
CD2 B:DAH513 4.2 13.0 0.6
CG2 B:VAL359 4.2 33.4 1.0
NE2 B:HIS103 4.4 12.3 1.0
CE1 B:DAH513 4.4 12.7 0.4
CE1 B:DAH513 4.4 12.5 0.6
CG B:HIS67 4.5 12.3 1.0
CE2 B:PHE368 4.5 10.1 1.0
CB B:VAL359 4.5 23.2 1.0
NE2 B:HIS332 4.5 10.4 1.0
NE2 B:HIS328 4.7 11.0 1.0
CE1 B:HIS328 4.7 12.5 1.0
CA B:VAL359 4.7 14.2 1.0
CE1 B:HIS332 4.8 11.2 1.0
O B:VAL359 4.9 14.2 1.0
CZ B:PHE368 5.0 11.9 1.0

Copper binding site 7 out of 8 in 6ju5

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Copper binding site 7 out of 8 in the Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y 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 Pro-Tyrosinase C92A/F513Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:12.5
occ:0.50
CU B:CU702 0.0 12.5 0.5
CU B:CU702 0.7 13.5 0.4
NE2 B:HIS332 1.9 10.4 1.0
NE2 B:HIS372 1.9 11.2 1.0
O B:HOH847 2.3 23.1 1.0
NE2 B:HIS328 2.3 11.0 1.0
CD2 B:HIS372 2.8 12.3 1.0
CE1 B:HIS332 2.8 11.2 1.0
CE1 B:HIS372 2.9 10.2 1.0
CD2 B:HIS332 2.9 10.5 1.0
CD2 B:HIS328 3.0 10.3 1.0
CE1 B:HIS328 3.4 12.5 1.0
CE2 B:PHE368 3.6 10.1 1.0
CG B:HIS372 4.0 10.7 1.0
ND1 B:HIS372 4.0 10.2 1.0
CD2 B:HIS371 4.0 12.1 1.0
ND1 B:HIS332 4.0 10.3 1.0
OZ B:DAH513 4.0 15.8 0.6
OE2 B:DAH513 4.1 16.5 0.6
CG B:HIS332 4.1 9.0 1.0
CU B:CU701 4.1 17.6 0.3
CD2 B:PHE368 4.2 9.7 1.0
CG B:HIS328 4.2 11.2 1.0
OH B:DAH513 4.3 16.3 0.4
CZ B:PHE368 4.3 11.9 1.0
ND1 B:HIS328 4.4 12.7 1.0
NE2 B:HIS371 4.4 10.9 1.0
CZ B:DAH513 4.4 12.2 0.6
CE2 B:DAH513 4.5 14.1 0.6
CU B:CU701 4.5 16.8 0.5
CE2 B:DAH513 4.6 14.0 0.4
CZ B:DAH513 4.6 12.9 0.4
NE2 B:HIS103 5.0 12.3 1.0

Copper binding site 8 out of 8 in 6ju5

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Copper binding site 8 out of 8 in the Aspergillus Oryzae Pro-Tyrosinase C92A/F513Y 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 Pro-Tyrosinase C92A/F513Y Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:13.5
occ:0.43
CU B:CU702 0.0 13.5 0.4
CU B:CU702 0.7 12.5 0.5
O B:HOH847 1.9 23.1 1.0
NE2 B:HIS328 1.9 11.0 1.0
NE2 B:HIS372 2.1 11.2 1.0
NE2 B:HIS332 2.1 10.4 1.0
CE1 B:HIS372 2.9 10.2 1.0
CE1 B:HIS328 2.9 12.5 1.0
CD2 B:HIS328 2.9 10.3 1.0
CD2 B:HIS332 3.1 10.5 1.0
CE1 B:HIS332 3.2 11.2 1.0
CD2 B:HIS372 3.2 12.3 1.0
OE2 B:DAH513 3.5 16.5 0.6
CU B:CU701 3.6 17.6 0.3
OZ B:DAH513 3.7 15.8 0.6
CE2 B:PHE368 3.9 10.1 1.0
ND1 B:HIS328 4.0 12.7 1.0
CE2 B:DAH513 4.0 14.1 0.6
OH B:DAH513 4.0 16.3 0.4
CG B:HIS328 4.0 11.2 1.0
CU B:CU701 4.0 16.8 0.5
CE2 B:DAH513 4.1 14.0 0.4
ND1 B:HIS372 4.1 10.2 1.0
CZ B:DAH513 4.1 12.2 0.6
ND1 B:HIS332 4.2 10.3 1.0
CG B:HIS332 4.2 9.0 1.0
CG B:HIS372 4.3 10.7 1.0
CZ B:DAH513 4.3 12.9 0.4
CZ B:PHE368 4.5 11.9 1.0
CD2 B:HIS371 4.6 12.1 1.0
NE2 B:HIS103 4.6 12.3 1.0
CD2 B:PHE368 4.6 9.7 1.0
NE2 B:HIS67 4.8 15.9 1.0
NE2 B:HIS371 4.8 10.9 1.0
NE2 B:HIS94 4.8 19.0 1.0
CE1 B:PHE99 4.8 10.7 1.0
CD2 B:HIS103 4.9 11.8 1.0
CD2 B:DAH513 5.0 13.4 0.4
CD2 B:DAH513 5.0 13.0 0.6

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 06:19:20 2024

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