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Copper in PDB 3ta4: Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane

Enzymatic activity of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane

All present enzymatic activity of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane:
1.10.3.2;

Protein crystallography data

The structure of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane, PDB code: 3ta4 was solved by T.Lukk, S.Majumdar, J.A.Gerlt, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 2.35
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.420, 115.260, 163.510, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.8

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Copper atom in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane (pdb code 3ta4). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 16 binding sites of Copper where determined in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane, PDB code: 3ta4:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 16 in 3ta4

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Copper binding site 1 out of 16 in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu307

b:52.2
occ:1.00
 NE2 F:HIS222 2.1 26.1 1.0
NE2 E:HIS90 2.2 19.6 1.0
O E:HOH366 2.6 12.8 1.0
CD2 F:HIS222 2.9 22.7 1.0
O E:HOH359 3.0 35.8 1.0
CD2 E:HIS90 3.1 20.6 1.0
CE1 E:HIS90 3.2 21.0 1.0
CE1 F:HIS222 3.2 22.6 1.0
CD2 F:HIS224 3.3 31.6 1.0
NE2 F:HIS224 3.4 30.8 1.0
NE2 E:HIS92 3.7 24.9 1.0
CU F:CU309 3.8 27.3 1.0
CU E:CU308 3.8 28.0 1.0
CD2 E:HIS92 4.0 24.4 1.0
CE1 E:HIS92 4.1 23.3 1.0
CG F:HIS222 4.1 27.3 1.0
CG F:HIS224 4.1 33.7 1.0
ND1 F:HIS222 4.2 27.6 1.0
CE1 F:HIS224 4.2 31.4 1.0
ND1 E:HIS90 4.3 26.0 1.0
CG E:HIS90 4.3 24.6 1.0
O E:PRO91 4.3 18.6 1.0
CG E:HIS92 4.5 26.9 1.0
ND1 E:HIS92 4.5 25.1 1.0
OH E:TYR96 4.6 25.7 1.0
ND1 F:HIS224 4.6 32.3 1.0
NE2 F:HIS275 4.8 23.9 1.0
NE2 E:HIS146 4.8 21.8 1.0
CA F:HIS224 4.8 31.5 1.0
NE2 F:HIS277 4.8 31.5 1.0
CD2 E:HIS146 4.9 22.1 1.0

Copper binding site 2 out of 16 in 3ta4

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Copper binding site 2 out of 16 in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu309

b:27.3
occ:1.00
 NE2 F:HIS224 2.0 30.8 1.0
NE2 E:HIS146 2.2 21.8 1.0
NE2 F:HIS275 2.2 23.9 1.0
O E:HOH366 2.4 12.8 1.0
CE1 F:HIS224 2.9 31.4 1.0
CE1 E:HIS146 2.9 22.0 1.0
CD2 F:HIS275 3.1 24.3 1.0
CE1 F:HIS275 3.1 23.6 1.0
CD2 F:HIS224 3.1 31.6 1.0
CD2 E:HIS146 3.3 22.1 1.0
O E:HOH396 3.4 34.5 1.0
CE F:MET273 3.6 59.4 1.0
CU F:CU307 3.8 52.2 1.0
ND1 F:HIS224 4.1 32.3 1.0
ND1 F:HIS275 4.1 27.1 1.0
CG F:HIS275 4.1 25.9 1.0
CD2 F:HIS222 4.1 22.7 1.0
ND1 E:HIS146 4.1 24.8 1.0
CG F:HIS224 4.2 33.7 1.0
NE2 E:HIS90 4.3 19.6 1.0
CG E:HIS146 4.4 24.1 1.0
CD2 E:HIS152 4.4 25.7 1.0
NE2 F:HIS222 4.6 26.1 1.0
CE1 E:HIS90 4.8 21.0 1.0
CD2 E:HIS90 4.8 20.6 1.0
SD F:MET273 4.8 61.0 1.0
CG F:MET273 4.8 46.1 1.0

Copper binding site 3 out of 16 in 3ta4

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Copper binding site 3 out of 16 in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu310

b:25.4
occ:1.00
 ND1 F:HIS219 2.0 21.6 1.0
SG F:CYS276 2.1 22.6 1.0
ND1 F:HIS281 2.1 23.0 1.0
CE1 F:HIS219 3.0 20.1 1.0
CG F:HIS219 3.0 21.3 1.0
CG F:HIS281 3.1 24.0 1.0
CE1 F:HIS281 3.1 23.0 1.0
CB F:CYS276 3.2 20.2 1.0
CB F:HIS281 3.3 24.8 1.0
CB F:HIS219 3.4 21.9 1.0
O F:PHE218 3.5 26.1 1.0
SD F:MET286 3.5 34.0 1.0
CA F:HIS219 3.6 23.3 1.0
CG2 F:VAL278 4.0 19.6 1.0
CB F:VAL278 4.0 21.6 1.0
NE2 F:HIS219 4.1 19.1 1.0
CD2 F:HIS219 4.2 17.5 1.0
CE F:MET286 4.2 27.6 1.0
NE2 F:HIS281 4.2 24.3 1.0
CD2 F:HIS281 4.2 22.8 1.0
C F:PHE218 4.3 27.4 1.0
N F:HIS219 4.5 25.4 1.0
CA F:CYS276 4.6 20.4 1.0
N F:THR220 4.6 24.2 1.0
C F:HIS219 4.7 23.4 1.0
CD2 F:PHE183 4.8 22.2 1.0
CG1 F:VAL278 4.8 20.6 1.0
CA F:HIS281 4.9 25.7 1.0
N F:VAL278 5.0 21.1 1.0
CE2 F:PHE183 5.0 21.9 1.0

Copper binding site 4 out of 16 in 3ta4

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Copper binding site 4 out of 16 in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu308

b:24.5
occ:1.00
 NE2 F:HIS92 2.0 10.6 1.0
NE2 D:HIS277 2.0 19.3 1.0
NE2 F:HIS144 2.1 16.9 1.0
O D:HOH365 2.7 16.8 1.0
CE1 F:HIS92 2.9 9.8 1.0
CD2 D:HIS277 2.9 20.4 1.0
CE1 D:HIS277 3.0 23.4 1.0
CD2 F:HIS92 3.0 11.9 1.0
CE1 F:HIS144 3.1 15.3 1.0
CD2 F:HIS144 3.2 15.9 1.0
CU D:CU307 3.7 69.3 1.0
CE1 F:HIS142 3.7 26.4 1.0
ND1 F:HIS92 4.0 15.1 1.0
ND1 D:HIS277 4.1 23.7 1.0
CG D:HIS277 4.1 21.4 1.0
CG F:HIS92 4.1 16.2 1.0
ND1 F:HIS144 4.2 16.5 1.0
CG F:HIS144 4.3 17.3 1.0
NE2 F:HIS142 4.3 23.9 1.0
NE2 D:HIS222 4.4 17.4 1.0
CD2 F:HIS90 4.4 19.7 1.0
CD2 D:HIS222 4.5 19.4 1.0
NE2 F:HIS90 4.6 22.1 1.0
CA F:GLY254 4.6 29.7 1.0
ND1 F:HIS142 4.6 24.3 1.0
CE1 F:HIS214 4.7 16.9 1.0
O F:GLY254 4.9 31.0 1.0

Copper binding site 5 out of 16 in 3ta4

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Copper binding site 5 out of 16 in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu1

b:63.5
occ:1.00
 OE1 F:GLU49 2.3 37.8 1.0
NE2 F:HIS193 2.4 60.1 1.0
CE1 F:HIS193 2.6 59.6 1.0
OE2 F:GLU49 2.7 38.6 1.0
CD F:GLU49 2.8 36.1 1.0
CD2 F:HIS193 3.6 58.8 1.0
ND1 F:HIS193 3.8 61.2 1.0
CG F:GLU49 4.3 32.7 1.0
CG F:HIS193 4.4 58.8 1.0
CB F:ALA192 4.7 41.2 1.0

Copper binding site 6 out of 16 in 3ta4

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Copper binding site 6 out of 16 in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu311

b:80.7
occ:1.00
 NE2 F:HIS306 2.4 78.3 1.0
CE1 F:HIS306 3.3 78.4 1.0
CD2 F:HIS306 3.4 76.3 1.0
ND1 F:HIS306 4.4 77.3 1.0
CG F:HIS306 4.5 75.6 1.0

Copper binding site 7 out of 16 in 3ta4

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Copper binding site 7 out of 16 in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu307

b:69.3
occ:1.00
 NE2 F:HIS90 2.1 22.1 1.0
NE2 D:HIS222 2.3 17.4 1.0
O D:HOH365 2.5 16.8 1.0
CE1 F:HIS90 3.0 22.5 1.0
CD2 D:HIS222 3.1 19.4 1.0
CD2 F:HIS90 3.1 19.7 1.0
O F:HOH358 3.2 23.9 1.0
NE2 D:HIS224 3.3 22.6 1.0
CD2 D:HIS224 3.3 23.3 1.0
CE1 D:HIS222 3.4 16.5 1.0
NE2 F:HIS92 3.4 10.6 1.0
CU D:CU309 3.6 24.6 1.0
CU F:CU308 3.7 24.5 1.0
CE1 F:HIS92 3.7 9.8 1.0
CD2 F:HIS92 3.9 11.9 1.0
ND1 F:HIS90 4.1 22.6 1.0
O F:PRO91 4.1 22.8 1.0
CE1 D:HIS224 4.1 21.8 1.0
CG F:HIS90 4.2 22.6 1.0
CG D:HIS224 4.2 22.4 1.0
CG D:HIS222 4.3 22.3 1.0
ND1 F:HIS92 4.3 15.1 1.0
ND1 D:HIS222 4.4 21.3 1.0
CG F:HIS92 4.4 16.2 1.0
OH F:TYR96 4.6 23.0 1.0
ND1 D:HIS224 4.6 23.5 1.0
CD2 F:HIS146 4.8 25.8 1.0
NE2 D:HIS277 4.8 19.3 1.0
NE2 F:HIS146 4.9 27.5 1.0
NE2 D:HIS275 4.9 25.8 1.0
NE2 F:HIS144 4.9 16.9 1.0
C F:PRO91 5.0 22.1 1.0
CD2 D:HIS277 5.0 20.4 1.0

Copper binding site 8 out of 16 in 3ta4

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Copper binding site 8 out of 16 in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu309

b:24.6
occ:1.00
 NE2 D:HIS224 2.1 22.6 1.0
NE2 D:HIS275 2.2 25.8 1.0
NE2 F:HIS146 2.2 27.5 1.0
O D:HOH365 2.5 16.8 1.0
CE1 D:HIS224 3.0 21.8 1.0
CD2 D:HIS275 3.1 21.8 1.0
CD2 D:HIS224 3.2 23.3 1.0
CE1 D:HIS275 3.2 24.4 1.0
CD2 F:HIS146 3.2 25.8 1.0
CE1 F:HIS146 3.2 24.2 1.0
CU D:CU307 3.6 69.3 1.0
CD2 D:HIS222 4.1 19.4 1.0
ND1 D:HIS224 4.1 23.5 1.0
SD D:MET273 4.2 43.2 1.0
CG D:HIS224 4.3 22.4 1.0
ND1 D:HIS275 4.3 23.5 1.0
CG D:HIS275 4.3 22.6 1.0
ND1 F:HIS146 4.3 25.7 1.0
CG F:HIS146 4.3 25.8 1.0
NE2 F:HIS90 4.3 22.1 1.0
NE2 D:HIS222 4.5 17.4 1.0
CE1 F:HIS90 4.7 22.5 1.0
CD2 F:HIS90 4.9 19.7 1.0
CD2 F:HIS152 4.9 25.9 1.0

Copper binding site 9 out of 16 in 3ta4

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Copper binding site 9 out of 16 in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu310

b:25.4
occ:1.00
 ND1 D:HIS281 2.1 18.5 1.0
ND1 D:HIS219 2.1 20.9 1.0
SG D:CYS276 2.2 23.6 1.0
CG D:HIS281 3.1 20.7 1.0
CE1 D:HIS219 3.1 21.7 1.0
CE1 D:HIS281 3.1 22.1 1.0
CG D:HIS219 3.1 22.8 1.0
CB D:CYS276 3.3 21.8 1.0
CB D:HIS281 3.3 21.1 1.0
CB D:HIS219 3.4 19.5 1.0
SD D:MET286 3.4 33.9 1.0
O D:PHE218 3.5 19.1 1.0
CA D:HIS219 3.6 21.6 1.0
CB D:VAL278 4.1 25.2 1.0
CG2 D:VAL278 4.1 22.7 1.0
NE2 D:HIS281 4.2 21.0 1.0
NE2 D:HIS219 4.2 22.9 1.0
CD2 D:HIS281 4.2 18.4 1.0
CD2 D:HIS219 4.2 23.9 1.0
C D:PHE218 4.3 20.4 1.0
CE D:MET286 4.3 28.3 1.0
N D:HIS219 4.4 22.0 1.0
N D:THR220 4.6 20.4 1.0
C D:HIS219 4.6 22.1 1.0
CA D:CYS276 4.7 21.4 1.0
CG1 D:VAL278 4.8 24.2 1.0
CA D:HIS281 4.9 23.1 1.0
CE D:MET186 4.9 42.0 1.0
CG D:MET286 4.9 28.7 1.0
CD2 D:PHE183 5.0 24.2 1.0

Copper binding site 10 out of 16 in 3ta4

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Copper binding site 10 out of 16 in the Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Small Laccase From Amycolatopsis Sp. Atcc 39116 Complexed with 1-(3,4- Dimethoxyphenyl)-2-(2-Methoxyphenoxy)-1,3-Dihydroxypropane within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu308

b:60.5
occ:1.00
 NE2 D:HIS90 2.0 28.6 1.0
NE2 E:HIS222 2.2 29.3 1.0
O E:HOH367 2.7 18.7 1.0
O D:HOH336 2.9 21.7 1.0
CE1 D:HIS90 2.9 26.0 1.0
CD2 D:HIS90 3.1 25.4 1.0
CD2 E:HIS222 3.2 28.1 1.0
CE1 E:HIS222 3.2 27.7 1.0
NE2 E:HIS224 3.5 24.7 1.0
CD2 E:HIS224 3.5 25.7 1.0
NE2 D:HIS92 3.7 21.6 1.0
CU E:CU309 3.8 26.2 1.0
CU D:CU311 3.8 25.4 1.0
O D:PRO91 4.0 18.7 1.0
CE1 D:HIS92 4.0 21.4 1.0
ND1 D:HIS90 4.0 29.0 1.0
CD2 D:HIS92 4.1 21.8 1.0
CG D:HIS90 4.1 24.3 1.0
CE1 E:HIS224 4.2 21.2 1.0
CG E:HIS224 4.2 25.2 1.0
ND1 E:HIS222 4.3 30.9 1.0
CG E:HIS222 4.3 28.8 1.0
ND1 D:HIS92 4.5 24.1 1.0
OH D:TYR96 4.5 30.3 1.0
CG D:HIS92 4.5 23.3 1.0
ND1 E:HIS224 4.5 24.0 1.0
O E:HOH373 4.9 32.8 1.0
NE2 E:HIS277 4.9 24.1 1.0
CD2 D:HIS146 4.9 18.7 1.0
CA E:HIS224 4.9 24.7 1.0
C D:PRO91 4.9 19.2 1.0
NE2 E:HIS275 5.0 23.4 1.0

Reference:

S.Majumdar, T.Lukk, J.O.Solbiati, S.Bauer, S.K.Nair, J.E.Cronan, J.A.Gerlt. Roles of Small Laccases From Streptomyces in Lignin Degradation. Biochemistry V. 53 4047 2014.
ISSN: ISSN 0006-2960
PubMed: 24870309
DOI: 10.1021/BI500285T
Page generated: Wed Jul 31 02:08:08 2024

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