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Copper in PDB 8bbr: Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum

Enzymatic activity of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum

All present enzymatic activity of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum:
1.14.18.1;

Protein crystallography data

The structure of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum, PDB code: 8bbr was solved by M.Fekry, K.Dave, D.Badgujar, O.Aurelius, E.Hamnevik, D.Dobritzsch, H.Danielson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 116.37 / 1.64
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.298, 63.443, 117.311, 90, 97.25, 90
R / Rfree (%) 19 / 22.4

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Copper atom in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum (pdb code 8bbr). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 11 binding sites of Copper where determined in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum, PDB code: 8bbr:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 11 in 8bbr

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Copper binding site 1 out of 11 in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:42.1
occ:0.70
 NE2 A:HIS80 2.1 32.3 1.0
O A:HOH695 2.1 37.3 1.0
NE2 A:HIS95 2.2 30.9 1.0
NE2 A:HIS86 2.2 53.1 0.9
CD2 A:HIS80 3.0 29.4 1.0
CE1 A:HIS95 3.0 29.5 1.0
CD2 A:HIS86 3.1 47.1 0.9
CE1 A:HIS80 3.2 30.4 1.0
CE1 A:HIS86 3.3 45.5 0.9
CD2 A:HIS95 3.3 26.3 1.0
CU A:CU402 3.7 25.9 0.9
CE2 A:PHE280 4.0 26.2 1.0
CB A:CYS84 4.0 31.2 1.0
CZ A:PHE280 4.0 23.6 1.0
SG A:CYS84 4.1 42.1 0.7
CG A:HIS80 4.1 26.8 1.0
ND1 A:HIS80 4.2 27.8 1.0
ND1 A:HIS95 4.2 24.8 1.0
O A:HOH705 4.2 35.7 1.0
CG A:HIS86 4.3 49.0 0.9
ND1 A:HIS86 4.3 50.4 0.9
CG A:HIS95 4.4 26.1 1.0
NE2 A:HIS284 4.4 28.0 1.0
CZ3 A:TRP94 4.7 21.5 1.0
CE1 A:HIS284 4.8 26.8 1.0
NE2 A:HIS258 4.8 22.1 1.0
OG A:SER274 4.8 21.3 1.0
NE2 A:HIS262 5.0 19.7 1.0

Copper binding site 2 out of 11 in 8bbr

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Copper binding site 2 out of 11 in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:25.9
occ:0.92
 NE2 A:HIS262 2.0 19.7 1.0
NE2 A:HIS284 2.1 28.0 1.0
NE2 A:HIS258 2.1 22.1 1.0
O A:HOH695 2.5 37.3 1.0
CD2 A:HIS262 2.9 20.6 1.0
CE1 A:HIS262 2.9 22.8 1.0
CE1 A:HIS284 3.0 26.8 1.0
CD2 A:HIS258 3.1 20.9 1.0
CD2 A:HIS284 3.1 26.1 1.0
CE1 A:HIS258 3.1 20.0 1.0
CE2 A:PHE280 3.7 26.2 1.0
CU A:CU401 3.7 42.1 0.7
ND1 A:HIS262 4.0 23.0 1.0
CG A:HIS262 4.1 21.0 1.0
CD2 A:HIS283 4.1 21.5 1.0
ND1 A:HIS284 4.1 26.3 1.0
NE2 A:HIS95 4.2 30.9 1.0
CG A:HIS258 4.2 21.3 1.0
ND1 A:HIS258 4.2 23.4 1.0
CG A:HIS284 4.2 23.8 1.0
CZ A:PHE280 4.3 23.6 1.0
NE2 A:HIS283 4.4 20.8 1.0
CD2 A:PHE280 4.4 26.5 1.0
CD2 A:HIS95 4.5 26.3 1.0
O A:HOH705 4.9 35.7 1.0

Copper binding site 3 out of 11 in 8bbr

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Copper binding site 3 out of 11 in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:49.5
occ:0.98
 NE2 A:HIS39 2.1 28.2 1.0
O A:HOH545 2.2 34.1 1.0
O A:HOH793 3.0 42.7 1.0
CD2 A:HIS39 3.0 25.3 1.0
CE1 A:HIS39 3.1 27.6 1.0
O A:LYS37 3.6 27.8 1.0
ND1 A:HIS39 4.2 23.4 1.0
CG A:HIS39 4.2 25.7 1.0
O A:HOH520 4.3 30.9 1.0
O A:ALA36 4.4 24.3 1.0
C A:LYS37 4.5 24.8 1.0

Copper binding site 4 out of 11 in 8bbr

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Copper binding site 4 out of 11 in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:61.7
occ:0.62
 O A:HOH624 1.9 44.4 1.0
OE1 A:GLU108 2.2 33.1 1.0
O A:HOH647 2.2 38.6 1.0
CU A:CU405 3.0 51.2 0.8
CD A:GLU108 3.1 32.8 1.0
O A:HOH782 3.4 49.9 1.0
OE2 A:GLU108 3.4 32.6 1.0
CG A:GLU108 4.5 28.3 1.0
O A:GLU108 5.0 22.3 1.0

Copper binding site 5 out of 11 in 8bbr

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Copper binding site 5 out of 11 in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:51.2
occ:0.79
 O A:HOH624 1.8 44.4 1.0
OE2 A:GLU108 2.0 32.6 1.0
O A:HOH647 2.7 38.6 1.0
CD A:GLU108 2.9 32.8 1.0
CU A:CU404 3.0 61.7 0.6
OE1 A:GLU108 3.2 33.1 1.0
O A:HOH760 3.8 37.0 1.0
O A:HOH773 3.9 32.3 1.0
CG A:GLU108 4.3 28.3 1.0
CB A:GLU108 4.8 24.5 1.0
CA A:GLU108 5.0 23.9 1.0

Copper binding site 6 out of 11 in 8bbr

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Copper binding site 6 out of 11 in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:47.9
occ:0.85
 O B:HOH704 1.9 44.4 1.0
NE2 B:HIS80 2.1 28.7 1.0
NE2 B:HIS95 2.1 31.1 1.0
NE2 B:HIS86 2.2 48.0 0.8
CD2 B:HIS80 2.9 24.7 1.0
CE1 B:HIS95 3.0 29.2 1.0
CE1 B:HIS80 3.2 25.8 1.0
CD2 B:HIS86 3.2 43.9 0.8
CE1 B:HIS86 3.2 40.6 0.8
CD2 B:HIS95 3.3 27.8 1.0
CU B:CU402 3.7 30.8 0.9
CB B:CYS84 3.9 35.3 1.0
SG B:CYS84 4.0 41.0 0.6
CE2 B:PHE280 4.0 27.8 1.0
CZ B:PHE280 4.1 27.8 1.0
CG B:HIS80 4.1 23.4 1.0
ND1 B:HIS95 4.2 29.4 1.0
ND1 B:HIS80 4.2 24.3 1.0
ND1 B:HIS86 4.3 42.7 0.8
CG B:HIS86 4.3 43.4 0.8
CG B:HIS95 4.4 28.3 1.0
NE2 B:HIS284 4.4 24.3 1.0
O B:HOH671 4.4 38.0 1.0
CE1 B:HIS284 4.7 24.4 1.0
CZ3 B:TRP94 4.7 22.6 1.0
NE2 B:HIS258 4.8 22.8 1.0
OG B:SER274 4.9 21.1 1.0

Copper binding site 7 out of 11 in 8bbr

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Copper binding site 7 out of 11 in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:30.8
occ:0.94
 NE2 B:HIS262 2.0 24.8 1.0
NE2 B:HIS284 2.1 24.3 1.0
NE2 B:HIS258 2.1 22.8 1.0
O B:HOH704 2.4 44.4 1.0
CE1 B:HIS284 3.0 24.4 1.0
CD2 B:HIS262 3.0 23.3 1.0
CE1 B:HIS262 3.0 25.6 1.0
CD2 B:HIS258 3.1 21.7 1.0
CD2 B:HIS284 3.1 24.8 1.0
CE1 B:HIS258 3.2 22.1 1.0
CE2 B:PHE280 3.7 27.8 1.0
CU B:CU401 3.7 47.9 0.8
CD2 B:HIS283 4.1 23.1 1.0
ND1 B:HIS262 4.1 24.4 1.0
ND1 B:HIS284 4.1 25.5 1.0
CG B:HIS262 4.1 22.3 1.0
CG B:HIS284 4.2 25.7 1.0
CG B:HIS258 4.2 22.8 1.0
NE2 B:HIS95 4.2 31.1 1.0
ND1 B:HIS258 4.2 23.6 1.0
CZ B:PHE280 4.3 27.8 1.0
NE2 B:HIS283 4.4 24.8 1.0
CD2 B:PHE280 4.4 27.5 1.0
CD2 B:HIS95 4.5 27.8 1.0
O B:HOH671 4.7 38.0 1.0
NE2 B:HIS80 5.0 28.7 1.0

Copper binding site 8 out of 11 in 8bbr

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Copper binding site 8 out of 11 in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:53.1
occ:1.00
 O B:HOH683 1.9 51.4 1.0
NE2 B:HIS39 2.0 33.9 1.0
CE1 B:HIS39 2.9 33.1 1.0
CD2 B:HIS39 3.0 31.6 1.0
O B:LYS37 3.3 29.4 1.0
ND1 B:HIS39 4.0 29.2 1.0
CG B:HIS39 4.1 28.9 1.0
C B:LYS37 4.1 29.0 1.0
O B:HOH520 4.1 36.6 1.0
O B:ALA36 4.3 33.0 1.0
CA B:LYS37 4.7 31.3 1.0
O B:HOH692 4.9 33.5 1.0

Copper binding site 9 out of 11 in 8bbr

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Copper binding site 9 out of 11 in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu404

b:49.6
occ:0.62
 O B:HOH607 1.8 38.9 1.0
OE1 B:GLU108 2.1 32.3 1.0
O B:HOH514 2.4 34.5 1.0
CD B:GLU108 2.9 34.7 1.0
OE2 B:GLU108 3.1 45.9 1.0
CU B:CU405 3.1 70.0 0.6
O B:HOH786 4.3 36.5 1.0
CG B:GLU108 4.4 30.7 1.0
O B:HOH759 4.9 48.1 1.0
CB B:GLU108 4.9 27.1 1.0

Copper binding site 10 out of 11 in 8bbr

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Copper binding site 10 out of 11 in the Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Determination of the Structure of Active Tyrosinase From Bacterium Verrucomicrobium Spinosum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu405

b:70.0
occ:0.59
 O B:HOH514 1.7 34.5 1.0
OE2 B:GLU108 2.1 45.9 1.0
O B:HOH607 2.2 38.9 1.0
O B:HOH759 2.9 48.1 1.0
CU B:CU404 3.1 49.6 0.6
CD B:GLU108 3.2 34.7 1.0
OE1 B:GLU108 3.6 32.3 1.0
CG B:GLU108 4.5 30.7 1.0

Reference:

M.Fekry, K.K.Dave, D.Badgujar, E.Hamnevik, O.Aurelius, D.Dobritzsch, U.H.Danielson. The Crystal Structure of Tyrosinase From Verrucomicrobium Spinosum Reveals It to Be An Atypical Bacterial Tyrosinase Biomolecules V. 13 2023.
ISSN: ESSN 2218-273X
DOI: 10.3390/BIOM13091360
Page generated: Wed Jul 31 09:33:08 2024

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