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Copper in PDB 3tbc: Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.

Enzymatic activity of Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.

All present enzymatic activity of Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.:
1.10.3.2;

Protein crystallography data

The structure of Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone., PDB code: 3tbc 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) 19.76 / 2.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.020, 127.020, 155.540, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 21

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. (pdb code 3tbc). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone., PDB code: 3tbc:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 3tbc

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Copper binding site 1 out of 12 in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.


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 Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu5

b:39.9
occ:1.00
 ND1 A:HIS288 2.0 39.8 1.0
ND1 A:HIS226 2.1 34.4 1.0
SG A:CYS283 2.3 41.4 1.0
CE A:MET293 2.6 0.5 1.0
CE1 A:HIS226 3.0 31.7 1.0
CG A:HIS288 3.0 39.8 1.0
CE1 A:HIS288 3.0 40.6 1.0
CG A:HIS226 3.2 36.9 1.0
CB A:CYS283 3.2 21.2 1.0
CB A:HIS288 3.3 35.1 1.0
CB A:HIS226 3.6 38.5 1.0
SD A:MET293 3.9 56.1 1.0
CA A:HIS226 4.0 40.2 1.0
NE2 A:HIS288 4.1 41.7 1.0
CD2 A:HIS288 4.1 39.0 1.0
NE2 A:HIS226 4.1 29.3 1.0
CG2 A:VAL285 4.1 33.7 1.0
CB A:VAL285 4.1 30.0 1.0
O A:TYR225 4.2 27.7 1.0
CD2 A:HIS226 4.2 35.2 1.0
CA A:CYS283 4.6 27.6 1.0
N A:THR227 4.8 39.2 1.0
CD2 A:PHE190 4.8 42.1 1.0
CA A:HIS288 4.8 34.3 1.0
CE2 A:PHE190 4.9 42.8 1.0
N A:VAL285 4.9 31.4 1.0
C A:HIS226 5.0 42.3 1.0
N A:HIS226 5.0 37.8 1.0
C A:TYR225 5.0 32.9 1.0

Copper binding site 2 out of 12 in 3tbc

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Copper binding site 2 out of 12 in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.


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 Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu8

b:47.1
occ:1.00
 NE2 B:HIS153 2.1 33.2 1.0
NE2 A:HIS231 2.1 34.3 1.0
NE2 A:HIS282 2.3 40.7 1.0
O1 A:OXY1 2.3 61.4 1.0
O2 A:OXY1 2.4 63.7 1.0
CE1 A:HIS231 2.9 29.2 1.0
CE1 B:HIS153 3.0 35.6 1.0
CD2 A:HIS282 3.1 37.4 1.0
CD2 B:HIS153 3.1 31.4 1.0
CE1 A:HIS282 3.2 36.1 1.0
CD2 A:HIS231 3.3 35.8 1.0
O B:HOH352 3.7 45.2 1.0
CD2 A:HIS229 4.0 39.4 1.0
ND1 A:HIS231 4.1 35.1 1.0
ND1 B:HIS153 4.1 36.6 1.0
CG B:HIS153 4.2 33.7 1.0
ND1 A:HIS282 4.2 36.2 1.0
CG A:HIS282 4.3 34.5 1.0
CG A:HIS231 4.3 36.4 1.0
NE2 A:HIS229 4.3 36.2 1.0
CD2 B:HIS159 4.4 41.0 1.0
NE2 B:HIS97 4.5 44.3 1.0
CE A:MET280 4.7 72.7 1.0
SD A:MET280 4.8 60.7 1.0
CB A:MET280 4.8 42.6 1.0
CE1 B:HIS97 4.9 46.0 1.0
CD2 B:HIS97 4.9 46.6 1.0
NE2 A:HIS284 5.0 45.5 1.0

Copper binding site 3 out of 12 in 3tbc

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Copper binding site 3 out of 12 in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.


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 Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu12

b:75.0
occ:1.00
 NE2 C:HIS284 2.2 34.6 1.0
NE2 A:HIS99 2.2 38.8 1.0
NE2 A:HIS151 2.3 39.1 1.0
O1 C:OXY348 2.8 63.7 1.0
CD2 C:HIS284 3.0 30.1 1.0
O2 C:OXY348 3.1 63.2 1.0
CE1 A:HIS151 3.1 43.4 1.0
CE1 A:HIS99 3.1 39.2 1.0
CE1 C:HIS284 3.2 33.1 1.0
CD2 A:HIS99 3.2 35.1 1.0
CD2 A:HIS151 3.4 42.4 1.0
CD2 A:HIS97 4.0 45.0 1.0
NE2 C:HIS229 4.0 49.8 1.0
CB A:ALA261 4.1 29.4 1.0
CU C:CU347 4.1 0.8 1.0
CG C:HIS284 4.1 30.3 1.0
CD2 C:HIS229 4.2 46.1 1.0
ND1 C:HIS284 4.2 31.4 1.0
ND1 A:HIS99 4.3 43.3 1.0
CE1 A:HIS149 4.3 37.4 1.0
ND1 A:HIS151 4.3 44.2 1.0
NE2 A:HIS97 4.3 43.5 1.0
CG A:HIS99 4.3 34.4 1.0
CG A:HIS151 4.5 41.5 1.0
CE1 C:HIS229 4.7 48.2 1.0
NE2 A:HIS149 4.9 36.1 1.0

Copper binding site 4 out of 12 in 3tbc

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Copper binding site 4 out of 12 in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.


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 Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu344

b:0.2
occ:1.00
 NE2 B:HIS229 2.0 47.9 1.0
NE2 C:HIS97 2.1 47.5 1.0
CE1 B:HIS229 2.9 46.0 1.0
CD2 C:HIS97 3.0 45.3 1.0
CE1 C:HIS97 3.0 51.9 1.0
CD2 B:HIS229 3.1 44.4 1.0
O C:HOH424 3.5 45.2 1.0
NE2 B:HIS231 3.6 42.2 1.0
CE1 C:HIS99 3.7 37.9 1.0
CD2 B:HIS231 3.7 40.1 1.0
CU C:CU344 3.7 75.9 1.0
CE1 B:HIS231 3.9 43.5 1.0
NE2 C:HIS99 3.9 41.3 1.0
CG B:HIS231 4.0 40.9 1.0
ND1 C:HIS99 4.0 38.6 1.0
ND1 B:HIS229 4.1 44.0 1.0
ND1 B:HIS231 4.1 41.9 1.0
CU B:CU345 4.1 56.0 1.0
ND1 C:HIS97 4.1 52.6 1.0
CG C:HIS97 4.2 47.1 1.0
CG B:HIS229 4.2 44.5 1.0
O C:VAL98 4.3 39.8 1.0
OH C:TYR103 4.3 47.9 1.0
CD2 C:HIS99 4.3 38.3 1.0
CG C:HIS99 4.4 41.1 1.0
CA B:HIS231 4.6 41.4 1.0
OD2 B:ASP254 4.8 42.6 1.0
O B:HOH429 4.9 50.1 1.0
CB B:HIS231 4.9 41.4 1.0
N B:HIS231 4.9 40.1 1.0

Copper binding site 5 out of 12 in 3tbc

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Copper binding site 5 out of 12 in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.


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 Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu345

b:56.0
occ:1.00
 O C:HOH424 2.1 45.2 1.0
NE2 B:HIS282 2.2 50.3 1.0
NE2 C:HIS153 2.2 40.3 1.0
NE2 B:HIS231 2.3 42.2 1.0
CE1 C:HIS153 3.0 38.1 1.0
CE1 B:HIS231 3.0 43.5 1.0
CE1 B:HIS282 3.1 48.9 1.0
CD2 B:HIS282 3.2 46.9 1.0
CD2 C:HIS153 3.4 36.7 1.0
CD2 B:HIS231 3.4 40.1 1.0
O C:HOH441 4.0 56.6 1.0
CU B:CU344 4.1 0.2 1.0
CD2 B:HIS229 4.1 44.4 1.0
ND1 C:HIS153 4.2 36.3 1.0
ND1 B:HIS231 4.2 41.9 1.0
ND1 B:HIS282 4.2 45.8 1.0
CG B:HIS282 4.3 43.9 1.0
CG C:HIS153 4.4 36.9 1.0
CG B:HIS231 4.4 40.9 1.0
NE2 B:HIS229 4.5 47.9 1.0
NE2 C:HIS97 4.6 47.5 1.0
ND1 C:HIS159 4.6 45.8 1.0
SD B:MET280 4.7 58.8 1.0
CU C:CU344 4.8 75.9 1.0
CE B:MET280 4.8 0.6 1.0
NE2 B:HIS284 4.9 35.5 1.0
CD2 C:HIS97 4.9 45.3 1.0

Copper binding site 6 out of 12 in 3tbc

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Copper binding site 6 out of 12 in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.


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 Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu346

b:36.8
occ:1.00
 ND1 B:HIS288 2.0 36.4 1.0
ND1 B:HIS226 2.1 36.5 1.0
SG B:CYS283 2.2 44.3 1.0
CE1 B:HIS288 3.0 33.6 1.0
CG B:HIS226 3.0 39.0 1.0
CG B:HIS288 3.1 37.9 1.0
CB B:CYS283 3.1 31.3 1.0
CE1 B:HIS226 3.1 35.6 1.0
CB B:HIS226 3.3 37.9 1.0
CE B:MET293 3.4 95.1 1.0
CB B:HIS288 3.4 37.7 1.0
SD B:MET293 3.5 42.3 1.0
CA B:HIS226 3.8 40.5 1.0
CG2 B:VAL285 3.9 26.4 1.0
CB B:VAL285 4.0 26.3 1.0
NE2 B:HIS288 4.1 34.0 1.0
CD2 B:HIS226 4.1 39.9 1.0
O B:TYR225 4.2 30.5 1.0
CD2 B:HIS288 4.2 37.6 1.0
NE2 B:HIS226 4.2 37.9 1.0
CA B:CYS283 4.5 33.5 1.0
N B:THR227 4.7 36.9 1.0
N B:HIS226 4.8 39.7 1.0
C B:HIS226 4.8 41.3 1.0
CG1 B:VAL285 4.9 21.6 1.0
CD2 B:PHE190 4.9 45.1 1.0
C B:TYR225 4.9 35.5 1.0
CA B:HIS288 4.9 43.0 1.0
N B:VAL285 5.0 37.7 1.0
CG B:MET293 5.0 39.7 1.0

Copper binding site 7 out of 12 in 3tbc

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Copper binding site 7 out of 12 in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.


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 Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu347

b:81.0
occ:1.00
 NE2 B:HIS151 2.2 37.1 1.0
NE2 B:HIS99 2.2 45.1 1.0
NE2 A:HIS284 2.3 45.5 1.0
O2 A:OXY1 2.8 63.7 1.0
O1 A:OXY1 2.9 61.4 1.0
CD2 A:HIS284 3.1 37.8 1.0
CD2 B:HIS151 3.1 37.4 1.0
CE1 B:HIS151 3.1 37.8 1.0
CE1 B:HIS99 3.2 44.9 1.0
CD2 B:HIS99 3.2 45.4 1.0
CE1 A:HIS284 3.4 43.4 1.0
CD2 B:HIS97 3.7 46.6 1.0
NE2 B:HIS97 4.0 44.3 1.0
NE2 A:HIS229 4.3 36.2 1.0
CB B:ALA261 4.3 31.5 1.0
ND1 B:HIS151 4.3 40.0 1.0
ND1 B:HIS99 4.3 45.1 1.0
CE1 B:HIS149 4.3 29.1 1.0
CG B:HIS151 4.3 42.1 1.0
CG B:HIS99 4.3 41.5 1.0
CG A:HIS284 4.3 33.4 1.0
ND1 A:HIS284 4.4 38.8 1.0
CD2 A:HIS229 4.5 39.4 1.0
CE1 A:HIS229 4.7 41.5 1.0
O B:HOH352 4.7 45.2 1.0
NE2 B:HIS149 4.9 24.4 1.0
CU B:CU348 4.9 0.7 1.0
CE1 B:HIS221 5.0 36.4 1.0

Copper binding site 8 out of 12 in 3tbc

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Copper binding site 8 out of 12 in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.


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 Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu348

b:0.7
occ:1.00
 NE2 B:HIS97 2.3 44.3 1.0
NE2 A:HIS229 2.5 36.2 1.0
CE1 A:HIS229 2.6 41.5 1.0
CE1 B:HIS97 2.7 46.0 1.0
OH B:TYR103 3.5 45.0 1.0
CD2 B:HIS97 3.6 46.6 1.0
O B:VAL98 3.6 37.5 1.0
CD2 A:HIS231 3.8 35.8 1.0
O A:HOH426 3.9 48.3 1.0
CA A:HIS231 3.9 34.3 1.0
CD2 A:HIS229 3.9 39.4 1.0
CG A:HIS231 3.9 36.4 1.0
ND1 B:HIS97 4.0 48.1 1.0
ND1 A:HIS229 4.0 41.2 1.0
O2 A:OXY1 4.0 63.7 1.0
OD2 A:ASP254 4.1 40.6 1.0
NE2 A:HIS231 4.2 34.3 1.0
CD2 B:HIS99 4.2 45.4 1.0
O A:LEU230 4.3 30.9 1.0
CG B:HIS99 4.3 41.5 1.0
NE2 B:HIS99 4.3 45.1 1.0
ND1 A:HIS231 4.3 35.1 1.0
CB A:HIS231 4.4 34.2 1.0
CA B:HIS99 4.4 35.7 1.0
CG B:HIS97 4.4 48.8 1.0
C B:VAL98 4.5 36.3 1.0
ND1 B:HIS99 4.5 45.1 1.0
CE1 B:HIS99 4.5 44.9 1.0
CE1 A:HIS231 4.5 29.2 1.0
N A:HIS231 4.5 33.5 1.0
CG A:HIS229 4.6 39.7 1.0
CZ B:TYR103 4.6 42.8 1.0
N A:GLY232 4.7 37.2 1.0
C A:LEU230 4.7 32.2 1.0
CG A:ASP254 4.7 38.2 1.0
N B:HIS99 4.8 36.4 1.0
C A:HIS231 4.8 34.8 1.0
CU B:CU347 4.9 81.0 1.0
O1 A:OXY1 4.9 61.4 1.0
CB B:HIS99 4.9 35.5 1.0

Copper binding site 9 out of 12 in 3tbc

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Copper binding site 9 out of 12 in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.


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 Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu344

b:75.9
occ:1.00
 NE2 C:HIS151 2.2 37.7 1.0
NE2 C:HIS99 2.3 41.3 1.0
NE2 B:HIS284 2.4 35.5 1.0
O C:HOH424 2.7 45.2 1.0
CE1 C:HIS151 3.0 40.2 1.0
CE1 C:HIS99 3.0 37.9 1.0
CD2 B:HIS284 3.3 31.6 1.0
CD2 C:HIS151 3.3 35.7 1.0
CD2 C:HIS99 3.4 38.3 1.0
CE1 B:HIS284 3.5 33.7 1.0
CU B:CU344 3.7 0.2 1.0
CD2 C:HIS97 3.9 45.3 1.0
ND1 C:HIS99 4.2 38.6 1.0
NE2 B:HIS229 4.2 47.9 1.0
ND1 C:HIS151 4.2 37.1 1.0
NE2 C:HIS97 4.3 47.5 1.0
CG C:HIS151 4.4 35.4 1.0
CD2 B:HIS229 4.4 44.4 1.0
CG C:HIS99 4.4 41.1 1.0
CB C:ALA261 4.4 28.7 1.0
CE1 C:HIS149 4.5 41.5 1.0
CG B:HIS284 4.5 31.5 1.0
ND1 B:HIS284 4.5 30.7 1.0
O C:HOH441 4.6 56.6 1.0
CU B:CU345 4.8 56.0 1.0
CE1 B:HIS229 4.9 46.0 1.0

Copper binding site 10 out of 12 in 3tbc

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Copper binding site 10 out of 12 in the Small Laccase From Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone.


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 Streptomyces Viridosporus T7A; Alternate Crystal Form Complexed with Acetovanillone. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu345

b:40.2
occ:1.00
 ND1 C:HIS288 2.0 40.4 1.0
ND1 C:HIS226 2.1 32.1 1.0
SG C:CYS283 2.3 35.8 1.0
CG C:HIS288 3.0 42.6 1.0
CE1 C:HIS288 3.0 42.0 1.0
CG C:HIS226 3.1 30.4 1.0
CE1 C:HIS226 3.1 29.4 1.0
CB C:CYS283 3.1 31.5 1.0
CB C:HIS288 3.2 38.4 1.0
CE C:MET293 3.4 62.1 1.0
CB C:HIS226 3.4 30.5 1.0
SD C:MET293 3.6 44.4 1.0
CA C:HIS226 3.8 34.1 1.0
CG2 C:VAL285 3.8 34.8 1.0
CB C:VAL285 3.9 35.5 1.0
CD2 C:HIS288 4.1 45.6 1.0
NE2 C:HIS288 4.1 45.8 1.0
O C:TYR225 4.2 29.2 1.0
NE2 C:HIS226 4.2 28.2 1.0
CD2 C:HIS226 4.2 30.2 1.0
CA C:CYS283 4.5 33.8 1.0
N C:THR227 4.7 29.5 1.0
CG1 C:VAL285 4.7 34.3 1.0
CA C:HIS288 4.8 37.4 1.0
N C:VAL285 4.8 40.9 1.0
C C:HIS226 4.8 35.1 1.0
N C:HIS226 4.8 30.9 1.0
C C:TYR225 4.9 32.4 1.0
CA C:VAL285 4.9 45.6 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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