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Copper in PDB 4n8u: Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629

Enzymatic activity of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629

All present enzymatic activity of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629:
1.10.3.2;

Protein crystallography data

The structure of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629, PDB code: 4n8u was solved by A.Gabdulkhakov, S.Tischenko, L.Yurevich, A.Lisov, A.Leontievsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.95 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.720, 79.600, 204.050, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.8

Other elements in 4n8u:

The structure of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 (pdb code 4n8u). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629, PDB code: 4n8u:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 4n8u

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Copper binding site 1 out of 9 in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:17.7
occ:1.00
 ND1 A:HIS290 1.9 12.2 1.0
ND1 A:HIS228 1.9 19.1 1.0
SG A:CYS285 2.1 19.2 1.0
CE1 A:HIS290 2.8 18.4 1.0
CE1 A:HIS228 2.8 12.7 1.0
CG A:HIS228 2.8 21.7 1.0
CG A:HIS290 2.9 10.3 1.0
CE A:MET295 3.2 17.1 1.0
CB A:HIS228 3.2 13.2 1.0
CB A:CYS285 3.3 6.2 1.0
CB A:HIS290 3.3 13.5 1.0
SD A:MET295 3.7 26.4 1.0
CA A:HIS228 3.8 9.1 1.0
NE2 A:HIS228 3.9 17.4 1.0
CD2 A:HIS228 3.9 21.0 1.0
NE2 A:HIS290 3.9 14.3 1.0
CG2 A:VAL287 4.0 10.1 1.0
CD2 A:HIS290 4.0 13.0 1.0
O A:TYR227 4.1 17.8 1.0
CB A:VAL287 4.2 12.7 1.0
CA A:CYS285 4.6 17.2 1.0
CA A:HIS290 4.7 10.7 1.0
N A:THR229 4.8 10.3 1.0
N A:HIS228 4.8 14.1 1.0
C A:TYR227 4.9 17.9 1.0
C A:HIS228 4.9 11.3 1.0

Copper binding site 2 out of 9 in 4n8u

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Copper binding site 2 out of 9 in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:20.1
occ:1.00
 NE2 A:HIS284 2.1 17.2 1.0
NE2 A:HIS233 2.2 17.6 1.0
NE2 B:HIS155 2.4 22.9 1.0
CE1 A:HIS233 2.8 16.4 1.0
CD2 A:HIS284 3.0 17.9 1.0
O A:HOH517 3.1 22.0 1.0
CE1 A:HIS284 3.1 15.5 1.0
O B:HOH516 3.2 8.6 1.0
CD2 B:HIS155 3.3 14.9 1.0
CD2 A:HIS233 3.4 17.1 1.0
CE1 B:HIS155 3.4 18.5 1.0
ND1 A:HIS233 3.9 10.7 1.0
CD2 A:HIS231 4.1 10.7 1.0
CG A:HIS284 4.2 20.3 1.0
ND1 A:HIS284 4.2 17.6 1.0
CG A:HIS233 4.2 14.8 1.0
SD A:MET282 4.3 49.4 1.0
O B:HOH517 4.4 23.1 1.0
NE2 A:HIS231 4.4 15.7 1.0
CD2 B:HIS161 4.4 15.9 1.0
ND1 B:HIS155 4.5 12.7 1.0
CG B:HIS155 4.5 15.7 1.0
NE2 B:HIS99 4.7 20.4 1.0
CB A:MET282 4.8 19.2 1.0
NE2 A:HIS286 5.0 7.6 1.0
CD2 B:HIS99 5.0 17.4 1.0

Copper binding site 3 out of 9 in 4n8u

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Copper binding site 3 out of 9 in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:18.5
occ:1.00
 NE2 A:HIS153 1.8 6.4 1.0
NE2 C:HIS286 2.0 7.5 1.0
NE2 A:HIS101 2.0 9.4 1.0
CD2 A:HIS153 2.8 7.1 1.0
CE1 A:HIS101 2.8 12.2 1.0
CE1 C:HIS286 2.9 9.6 1.0
CE1 A:HIS153 2.9 12.9 1.0
CD2 C:HIS286 3.0 13.4 1.0
CD2 A:HIS101 3.1 13.2 1.0
CE1 A:HIS99 3.8 16.4 1.0
CG A:HIS153 3.9 9.0 1.0
ND1 A:HIS153 3.9 13.6 1.0
ND1 C:HIS286 3.9 13.8 1.0
ND1 A:HIS101 4.0 13.7 1.0
CG C:HIS286 4.0 17.2 1.0
ND1 A:HIS99 4.0 21.2 1.0
NE2 C:HIS231 4.1 19.6 1.0
CB A:ALA263 4.1 11.8 1.0
CG A:HIS101 4.2 12.5 1.0
CD2 C:HIS231 4.2 17.3 1.0
O C:HOH501 4.3 14.0 1.0
CE1 A:HIS151 4.4 14.1 1.0
CE1 C:HIS231 4.8 13.3 1.0
CE1 A:HIS223 4.8 9.8 1.0
NE2 A:HIS151 4.9 12.9 1.0
CG C:HIS231 5.0 18.6 1.0

Copper binding site 4 out of 9 in 4n8u

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Copper binding site 4 out of 9 in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:18.6
occ:1.00
 ND1 B:HIS228 1.9 22.5 1.0
SG B:CYS285 2.0 17.1 1.0
ND1 B:HIS290 2.1 14.8 1.0
CE1 B:HIS228 2.8 14.4 1.0
CG B:HIS290 3.0 17.5 1.0
CG B:HIS228 3.0 10.9 1.0
CB B:CYS285 3.0 12.7 1.0
CB B:HIS290 3.1 17.9 1.0
CE1 B:HIS290 3.2 12.2 1.0
SD B:MET295 3.3 16.7 1.0
CB B:HIS228 3.5 11.4 1.0
NE2 B:HIS228 3.9 11.4 1.0
CD2 B:HIS228 4.0 15.9 1.0
CA B:HIS228 4.0 14.2 1.0
CD2 B:HIS290 4.2 15.1 1.0
CB B:VAL287 4.2 17.7 1.0
NE2 B:HIS290 4.2 9.3 1.0
CE B:MET295 4.3 12.5 1.0
CG2 B:VAL287 4.3 11.3 1.0
CA B:CYS285 4.4 13.8 1.0
O B:TYR227 4.4 21.0 1.0
CA B:HIS290 4.6 23.1 1.0
CG B:MET295 4.7 16.1 1.0
N B:THR229 4.8 13.8 1.0
N B:VAL287 4.9 11.1 1.0
CD2 B:PHE192 5.0 11.6 1.0
C B:CYS285 5.0 18.2 1.0
N B:HIS228 5.0 11.9 1.0

Copper binding site 5 out of 9 in 4n8u

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Copper binding site 5 out of 9 in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:28.3
occ:1.00
 NE2 B:HIS233 2.0 19.8 1.0
NE2 C:HIS155 2.3 22.2 1.0
NE2 B:HIS284 2.4 15.7 1.0
CE1 B:HIS233 2.8 22.8 1.0
CD2 B:HIS284 3.2 14.4 1.0
CD2 B:HIS233 3.2 18.2 1.0
CD2 C:HIS155 3.2 14.2 1.0
O B:HOH519 3.2 20.4 1.0
CE1 C:HIS155 3.3 19.6 1.0
CE1 B:HIS284 3.5 16.0 1.0
O C:HOH517 3.7 19.2 1.0
ND1 B:HIS233 4.0 16.5 1.0
ND1 B:HIS231 4.1 22.8 1.0
CG B:HIS233 4.2 16.1 1.0
NE2 C:HIS99 4.2 14.8 1.0
CE1 B:HIS231 4.3 21.8 1.0
CG C:HIS155 4.4 11.6 1.0
CG B:HIS284 4.4 17.3 1.0
ND1 C:HIS155 4.4 15.2 1.0
ND1 B:HIS284 4.5 18.4 1.0
CE1 C:HIS99 4.5 12.2 1.0
SD B:MET282 4.5 39.0 1.0
ND1 C:HIS161 4.6 17.4 1.0
CD2 C:HIS99 4.7 17.4 1.0
CB B:MET282 4.7 15.3 1.0
NE2 B:HIS286 4.9 16.8 1.0

Copper binding site 6 out of 9 in 4n8u

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Copper binding site 6 out of 9 in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:16.9
occ:1.00
 NE2 B:HIS101 2.0 9.8 1.0
NE2 B:HIS153 2.1 15.7 1.0
NE2 A:HIS286 2.1 7.6 1.0
O A:HOH517 2.4 22.0 1.0
CD2 B:HIS153 2.7 12.9 1.0
CE1 A:HIS286 2.7 6.2 1.0
CE1 B:HIS101 2.9 12.1 1.0
CD2 B:HIS101 2.9 10.4 1.0
CE1 B:HIS153 3.2 14.1 1.0
CD2 A:HIS286 3.3 10.8 1.0
CD2 B:HIS99 3.8 17.4 1.0
CE1 B:HIS151 3.9 14.8 1.0
ND1 A:HIS286 3.9 6.0 1.0
CG B:HIS153 4.0 15.7 1.0
ND1 B:HIS101 4.0 15.3 1.0
CG B:HIS101 4.1 11.8 1.0
CB B:ALA263 4.1 8.7 1.0
ND1 B:HIS153 4.2 13.8 1.0
NE2 B:HIS99 4.2 20.4 1.0
CG A:HIS286 4.2 11.7 1.0
O B:HOH516 4.3 8.6 1.0
NE2 A:HIS231 4.5 15.7 1.0
NE2 B:HIS151 4.6 15.7 1.0
CD2 A:HIS231 4.7 10.7 1.0
ND1 B:HIS151 4.8 13.2 1.0
CE1 B:HIS223 4.9 7.3 1.0

Copper binding site 7 out of 9 in 4n8u

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Copper binding site 7 out of 9 in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:20.2
occ:1.00
 ND1 C:HIS228 2.0 16.4 1.0
ND1 C:HIS290 2.1 15.5 1.0
SG C:CYS285 2.3 11.8 1.0
CG C:HIS228 2.9 11.8 1.0
CE1 C:HIS228 3.0 10.9 1.0
CE1 C:HIS290 3.1 16.2 1.0
SD C:MET295 3.1 27.6 1.0
CG C:HIS290 3.1 11.1 1.0
CB C:HIS228 3.1 16.1 1.0
CB C:CYS285 3.4 7.3 1.0
CB C:HIS290 3.4 13.4 1.0
CA C:HIS228 3.7 11.0 1.0
O C:TYR227 3.9 14.1 1.0
CD2 C:HIS228 4.0 13.3 1.0
NE2 C:HIS228 4.1 18.6 1.0
NE2 C:HIS290 4.2 12.8 1.0
CD2 C:HIS290 4.2 13.0 1.0
CE C:MET295 4.2 11.1 1.0
CB C:VAL287 4.3 15.7 1.0
CG2 C:VAL287 4.3 13.1 1.0
N C:HIS228 4.6 13.2 1.0
CG C:MET295 4.6 12.5 1.0
C C:TYR227 4.6 17.3 1.0
CA C:CYS285 4.7 10.7 1.0
N C:THR229 4.8 15.6 1.0
C C:HIS228 4.9 16.4 1.0
CA C:HIS290 4.9 15.9 1.0
CD2 C:PHE192 4.9 12.7 1.0
CE2 C:PHE192 4.9 12.7 1.0

Copper binding site 8 out of 9 in 4n8u

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Copper binding site 8 out of 9 in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu402

b:34.8
occ:1.00
 NE2 C:HIS233 2.0 18.7 1.0
NE2 A:HIS155 2.0 20.3 1.0
NE2 C:HIS284 2.6 13.8 1.0
CE1 C:HIS233 2.6 17.3 1.0
CE1 A:HIS155 2.9 17.3 1.0
CD2 A:HIS155 3.1 17.1 1.0
CD2 C:HIS233 3.2 21.9 1.0
CD2 C:HIS284 3.3 9.2 1.0
CE1 C:HIS284 3.7 11.8 1.0
CD2 C:HIS231 3.7 17.3 1.0
O C:HOH501 3.8 14.0 1.0
ND1 C:HIS233 3.8 14.6 1.0
ND1 A:HIS155 4.0 20.3 1.0
NE2 C:HIS231 4.1 19.6 1.0
SD C:MET282 4.1 20.0 1.0
NE2 A:HIS99 4.1 15.1 1.0
CG C:HIS233 4.1 21.8 1.0
CG A:HIS155 4.2 23.4 1.0
CE1 A:HIS99 4.3 16.4 1.0
ND1 A:HIS161 4.4 12.8 1.0
CG C:HIS284 4.5 15.2 1.0
ND1 C:HIS284 4.7 19.1 1.0
CD2 A:HIS99 4.8 17.3 1.0
CE C:MET282 4.9 19.7 1.0
CE1 A:HIS161 4.9 14.3 1.0
NE2 C:HIS286 4.9 7.5 1.0
CD2 C:HIS286 5.0 13.4 1.0
ND1 A:HIS99 5.0 21.2 1.0
CG C:HIS231 5.0 18.6 1.0
CB C:MET282 5.0 16.1 1.0

Copper binding site 9 out of 9 in 4n8u

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Copper binding site 9 out of 9 in the Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu403

b:22.7
occ:1.00
 NE2 C:HIS101 1.9 12.9 1.0
NE2 C:HIS153 2.1 15.2 1.0
NE2 B:HIS286 2.2 16.8 1.0
O B:HOH519 2.3 20.4 1.0
CE1 C:HIS101 2.8 19.0 1.0
CE1 B:HIS286 2.8 14.3 1.0
CD2 C:HIS101 2.9 14.6 1.0
CD2 C:HIS153 3.0 13.4 1.0
CE1 C:HIS153 3.1 12.3 1.0
CD2 B:HIS286 3.3 25.1 1.0
CE1 B:HIS231 3.7 21.8 1.0
ND1 B:HIS231 3.8 22.8 1.0
CD2 C:HIS99 3.9 17.4 1.0
CB C:ALA263 3.9 19.1 1.0
ND1 C:HIS101 3.9 15.8 1.0
ND1 B:HIS286 4.0 21.4 1.0
CG C:HIS101 4.0 16.5 1.0
CE1 C:HIS151 4.0 19.5 1.0
NE2 C:HIS99 4.2 14.8 1.0
CG C:HIS153 4.2 15.2 1.0
ND1 C:HIS153 4.2 16.6 1.0
CG B:HIS286 4.2 21.5 1.0
NE2 B:HIS231 4.7 18.5 1.0
ND1 C:HIS151 4.8 13.9 1.0
NE2 C:HIS151 4.8 16.5 1.0
O C:HOH517 4.9 19.2 1.0
CA C:ALA263 4.9 14.5 1.0

Reference:

A.Gabdulkhakov, S.Tischenko, L.Yurevich, A.Lisov, A.Leontievsky. Two-Domain Laccase From Streptomyces Viridochromogenes at 2.4 A Resolution AC629 To Be Published.
Page generated: Wed Jul 31 03:17:12 2024

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