Atomistry » Copper » PDB 3t6w-3x1n » 3ta4
Atomistry »
  Copper »
    PDB 3t6w-3x1n »
      3ta4 »

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

Go back to Copper Binding Sites List in 3ta4
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

Go back to Copper Binding Sites List in 3ta4
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

Go back to Copper Binding Sites List in 3ta4
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

Go back to Copper Binding Sites List in 3ta4
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

Go back to Copper Binding Sites List in 3ta4
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

Go back to Copper Binding Sites List in 3ta4
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

Go back to Copper Binding Sites List in 3ta4
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

Go back to Copper Binding Sites List in 3ta4
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

Go back to Copper Binding Sites List in 3ta4
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

Go back to Copper Binding Sites List in 3ta4
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: Sun Dec 13 11:12:24 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy