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Copper in PDB 3kw7: Crystal Structure of Lacb From Trametes Sp. AH28-2

Enzymatic activity of Crystal Structure of Lacb From Trametes Sp. AH28-2

All present enzymatic activity of Crystal Structure of Lacb From Trametes Sp. AH28-2:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Lacb From Trametes Sp. AH28-2, PDB code: 3kw7 was solved by H.H.Ge, M.K.Teng, L.W.Niu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.44
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 98.778, 98.778, 149.960, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 29.2

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Lacb From Trametes Sp. AH28-2 (pdb code 3kw7). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of Lacb From Trametes Sp. AH28-2, PDB code: 3kw7:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 3kw7

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Copper binding site 1 out of 8 in the Crystal Structure of Lacb From Trametes Sp. AH28-2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Lacb From Trametes Sp. AH28-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:46.9
occ:1.00
 ND1 A:HIS461 2.0 35.8 1.0
SG A:CYS456 2.1 41.7 1.0
ND1 A:HIS400 2.1 34.6 1.0
CE1 A:HIS461 3.0 36.7 1.0
CG A:HIS461 3.0 35.2 1.0
CE1 A:HIS400 3.1 36.3 1.0
CG A:HIS400 3.1 35.8 1.0
CB A:CYS456 3.2 39.0 1.0
CB A:HIS461 3.3 35.9 1.0
CD1 A:ILE458 3.3 33.0 1.0
CB A:HIS400 3.4 36.9 1.0
CD2 A:PHE466 3.8 28.5 1.0
CB A:ILE458 3.9 36.4 1.0
CE2 A:PHE466 4.1 28.5 1.0
CG1 A:ILE458 4.1 34.0 1.0
CA A:HIS400 4.1 36.9 1.0
NE2 A:HIS461 4.1 36.6 1.0
CD2 A:HIS461 4.2 34.6 1.0
NE2 A:HIS400 4.2 36.9 1.0
CD2 A:HIS400 4.3 35.2 1.0
CA A:CYS456 4.6 38.9 1.0
CG2 A:ILE458 4.7 36.4 1.0
CD A:PRO401 4.7 35.5 1.0
N A:ILE458 4.8 37.6 1.0
CA A:HIS461 4.8 35.9 1.0
O A:ILE458 4.8 37.7 1.0
CA A:ILE458 4.9 36.9 1.0
C A:HIS400 5.0 36.4 1.0
C A:CYS456 5.0 38.5 1.0

Copper binding site 2 out of 8 in 3kw7

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Copper binding site 2 out of 8 in the Crystal Structure of Lacb From Trametes Sp. AH28-2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Lacb From Trametes Sp. AH28-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:58.4
occ:1.00
 NE2 A:HIS403 1.9 33.8 1.0
NE2 A:HIS64 2.0 30.0 1.0
CE1 A:HIS403 2.7 33.6 1.0
CE1 A:HIS64 2.8 29.5 1.0
CD2 A:HIS403 2.9 35.5 1.0
CD2 A:HIS64 3.0 31.0 1.0
ND1 A:HIS66 3.4 32.2 1.0
CE1 A:HIS405 3.4 39.6 1.0
ND1 A:HIS405 3.5 37.6 1.0
NE2 A:HIS405 3.6 39.2 1.0
CG A:HIS66 3.7 32.5 1.0
CA A:HIS66 3.7 30.9 1.0
CE1 A:HIS66 3.8 33.2 1.0
CG A:HIS405 3.8 35.9 1.0
ND1 A:HIS403 3.8 34.5 1.0
N A:GLY67 3.9 31.0 1.0
CD2 A:HIS405 3.9 38.6 1.0
CG A:HIS403 3.9 34.3 1.0
ND1 A:HIS64 4.0 30.2 1.0
CG A:HIS64 4.1 30.4 1.0
CB A:HIS66 4.1 31.0 1.0
CD2 A:HIS66 4.2 33.7 1.0
NE2 A:HIS66 4.2 34.0 1.0
CU A:CU604 4.2 61.1 1.0
C A:HIS66 4.3 30.5 1.0
CU A:CU603 4.4 53.3 1.0
CA A:HIS405 4.5 33.2 1.0
CB A:HIS405 4.7 33.7 1.0
N A:HIS66 4.7 30.7 1.0
CA A:GLY67 5.0 32.3 1.0
O A:TRP65 5.0 31.2 1.0

Copper binding site 3 out of 8 in 3kw7

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Copper binding site 3 out of 8 in the Crystal Structure of Lacb From Trametes Sp. AH28-2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Lacb From Trametes Sp. AH28-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:53.3
occ:1.00
 NE2 A:HIS405 1.9 39.2 1.0
NE2 A:HIS455 1.9 42.2 1.0
NE2 A:HIS111 2.0 36.2 1.0
CE1 A:HIS405 2.6 39.6 1.0
CE1 A:HIS455 2.8 42.3 1.0
CD2 A:HIS455 3.0 40.9 1.0
CD2 A:HIS111 3.0 32.6 1.0
CE1 A:HIS111 3.1 36.4 1.0
CD2 A:HIS405 3.1 38.6 1.0
ND1 A:HIS405 3.8 37.6 1.0
CD2 A:HIS403 3.9 35.5 1.0
ND1 A:HIS455 3.9 40.5 1.0
CG A:HIS455 4.1 38.4 1.0
CG A:HIS405 4.1 35.9 1.0
ND1 A:HIS111 4.2 32.3 1.0
CG A:HIS111 4.2 32.3 1.0
CU A:CU602 4.4 58.4 1.0
CD2 A:HIS64 4.4 31.0 1.0
NE2 A:HIS403 4.5 33.8 1.0
NE2 A:HIS64 4.6 30.0 1.0
CD2 A:PHE453 4.6 30.4 1.0
NE2 A:HIS457 4.6 45.4 1.0
CE1 A:HIS109 4.7 33.1 1.0
CD2 A:HIS457 4.8 44.7 1.0
CG A:PRO79 4.8 36.6 1.0
CB A:PHE453 4.8 32.9 1.0
CD1 A:LEU462 4.9 37.8 1.0
CG A:HIS64 4.9 30.4 1.0
CU A:CU604 5.0 61.1 1.0

Copper binding site 4 out of 8 in 3kw7

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Copper binding site 4 out of 8 in the Crystal Structure of Lacb From Trametes Sp. AH28-2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Lacb From Trametes Sp. AH28-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:61.1
occ:1.00
 ND1 A:HIS66 1.9 32.2 1.0
NE2 A:HIS457 2.0 45.4 1.0
NE2 A:HIS109 2.1 33.1 1.0
CE1 A:HIS66 2.7 33.2 1.0
CE1 A:HIS457 2.8 46.0 1.0
CD2 A:HIS109 2.9 34.1 1.0
CG A:HIS66 3.0 32.5 1.0
CD2 A:HIS457 3.0 44.7 1.0
CE1 A:HIS109 3.1 33.1 1.0
CZ2 A:TRP107 3.5 35.1 1.0
CB A:HIS66 3.5 31.0 1.0
CE2 A:TRP107 3.8 36.4 1.0
NE2 A:HIS66 3.9 34.0 1.0
ND1 A:HIS457 4.0 45.0 1.0
NE1 A:TRP107 4.0 35.3 1.0
CD2 A:HIS64 4.0 31.0 1.0
CG A:HIS109 4.0 33.5 1.0
CD2 A:HIS66 4.0 33.7 1.0
ND1 A:HIS109 4.1 32.9 1.0
CB A:SER241 4.1 41.6 1.0
CG A:HIS457 4.1 41.8 1.0
CU A:CU602 4.2 58.4 1.0
CH2 A:TRP107 4.2 34.6 1.0
NE2 A:HIS64 4.4 30.0 1.0
CA A:HIS66 4.6 30.9 1.0
CD2 A:HIS403 4.6 35.5 1.0
NE2 A:HIS403 4.7 33.8 1.0
OG A:SER241 4.7 40.2 1.0
CD2 A:TRP107 4.8 37.4 1.0
CU A:CU603 5.0 53.3 1.0
CD1 A:TRP107 5.0 35.9 1.0

Copper binding site 5 out of 8 in 3kw7

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Copper binding site 5 out of 8 in the Crystal Structure of Lacb From Trametes Sp. AH28-2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Lacb From Trametes Sp. AH28-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:52.7
occ:1.00
 ND1 B:HIS400 2.1 36.8 1.0
SG B:CYS456 2.1 39.4 1.0
ND1 B:HIS461 2.1 37.0 1.0
CE1 B:HIS400 3.0 38.7 1.0
CG B:HIS400 3.0 37.6 1.0
CE1 B:HIS461 3.1 38.1 1.0
CG B:HIS461 3.1 36.4 1.0
CB B:CYS456 3.2 38.8 1.0
CB B:HIS400 3.3 38.4 1.0
CD1 B:ILE458 3.4 38.7 1.0
CB B:HIS461 3.4 36.3 1.0
CD2 B:PHE466 3.8 26.3 1.0
CB B:ILE458 4.0 38.1 1.0
CE2 B:PHE466 4.0 25.5 1.0
CA B:HIS400 4.0 38.4 1.0
NE2 B:HIS400 4.2 40.0 1.0
CG1 B:ILE458 4.2 37.4 1.0
NE2 B:HIS461 4.2 38.2 1.0
CD2 B:HIS400 4.2 37.8 1.0
CD2 B:HIS461 4.2 36.7 1.0
CA B:CYS456 4.6 39.0 1.0
CD B:PRO401 4.6 36.3 1.0
CG2 B:ILE458 4.8 37.4 1.0
C B:HIS400 4.9 37.6 1.0
N B:ILE458 4.9 38.8 1.0
CA B:HIS461 4.9 36.2 1.0
CA B:ILE458 5.0 38.4 1.0

Copper binding site 6 out of 8 in 3kw7

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Copper binding site 6 out of 8 in the Crystal Structure of Lacb From Trametes Sp. AH28-2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Lacb From Trametes Sp. AH28-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:61.0
occ:1.00
 NE2 B:HIS64 1.9 32.4 1.0
NE2 B:HIS403 1.9 36.6 1.0
CE1 B:HIS64 2.7 32.3 1.0
CE1 B:HIS403 2.7 37.2 1.0
CD2 B:HIS64 2.9 32.5 1.0
CD2 B:HIS403 3.0 38.0 1.0
CE1 B:HIS405 3.1 44.4 1.0
ND1 B:HIS405 3.2 42.3 1.0
NE2 B:HIS405 3.3 44.0 1.0
CG B:HIS405 3.4 39.7 1.0
CD2 B:HIS405 3.5 42.7 1.0
ND1 B:HIS66 3.8 30.8 1.0
ND1 B:HIS64 3.8 30.8 1.0
ND1 B:HIS403 3.9 37.1 1.0
CA B:HIS66 3.9 32.2 1.0
N B:GLY67 4.0 33.0 1.0
CG B:HIS64 4.0 31.1 1.0
CG B:HIS66 4.0 32.3 1.0
CG B:HIS403 4.0 36.3 1.0
CA B:HIS405 4.2 36.8 1.0
CE1 B:HIS66 4.2 34.2 1.0
CB B:HIS405 4.3 37.1 1.0
CB B:HIS66 4.4 32.3 1.0
CU B:CU603 4.4 51.3 1.0
CD2 B:HIS66 4.5 33.7 1.0
C B:HIS66 4.5 32.5 1.0
CU B:CU604 4.5 67.7 1.0
NE2 B:HIS66 4.6 34.9 1.0
N B:HIS405 4.8 35.2 1.0
N B:HIS66 4.9 31.5 1.0
O B:TRP65 4.9 31.4 1.0

Copper binding site 7 out of 8 in 3kw7

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Copper binding site 7 out of 8 in the Crystal Structure of Lacb From Trametes Sp. AH28-2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Lacb From Trametes Sp. AH28-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:51.3
occ:1.00
 NE2 B:HIS455 1.8 43.9 1.0
NE2 B:HIS405 1.8 44.0 1.0
NE2 B:HIS111 2.1 44.0 1.0
CE1 B:HIS405 2.5 44.4 1.0
CD2 B:HIS455 2.8 43.4 1.0
CE1 B:HIS455 2.8 43.4 1.0
CE1 B:HIS111 3.0 44.8 1.0
CD2 B:HIS405 3.0 42.7 1.0
CD2 B:HIS111 3.1 41.1 1.0
ND1 B:HIS405 3.7 42.3 1.0
ND1 B:HIS455 3.9 42.3 1.0
CD2 B:HIS403 3.9 38.0 1.0
CG B:HIS455 3.9 40.0 1.0
CG B:HIS405 4.0 39.7 1.0
ND1 B:HIS111 4.1 40.6 1.0
CD2 B:PHE453 4.2 30.3 1.0
CG B:HIS111 4.2 38.9 1.0
CD2 B:HIS64 4.4 32.5 1.0
CU B:CU602 4.4 61.0 1.0
NE2 B:HIS403 4.4 36.6 1.0
CB B:PHE453 4.6 32.9 1.0
NE2 B:HIS64 4.6 32.4 1.0
NE2 B:HIS457 4.7 45.7 1.0
CE1 B:HIS109 4.8 33.0 1.0
CG B:PHE453 4.8 32.1 1.0
CG B:PRO79 4.8 32.9 1.0
CD2 B:HIS457 4.8 44.5 1.0
CD1 B:LEU462 4.8 38.1 1.0

Copper binding site 8 out of 8 in 3kw7

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Copper binding site 8 out of 8 in the Crystal Structure of Lacb From Trametes Sp. AH28-2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Lacb From Trametes Sp. AH28-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:67.7
occ:1.00
 NE2 B:HIS457 1.9 45.7 1.0
ND1 B:HIS66 1.9 30.8 1.0
NE2 B:HIS109 2.2 32.1 1.0
CE1 B:HIS457 2.7 45.5 1.0
CE1 B:HIS66 2.7 34.2 1.0
CD2 B:HIS109 2.9 33.3 1.0
CD2 B:HIS457 2.9 44.5 1.0
CG B:HIS66 3.0 32.3 1.0
CE1 B:HIS109 3.2 33.0 1.0
CZ2 B:TRP107 3.4 33.6 1.0
CB B:HIS66 3.5 32.3 1.0
CE2 B:TRP107 3.8 34.1 1.0
ND1 B:HIS457 3.8 44.5 1.0
NE2 B:HIS66 3.9 34.9 1.0
NE1 B:TRP107 3.9 33.6 1.0
CG B:HIS457 4.0 42.1 1.0
CB B:SER241 4.0 41.1 1.0
CG B:HIS109 4.1 32.7 1.0
CD2 B:HIS66 4.1 33.7 1.0
CD2 B:HIS64 4.1 32.5 1.0
ND1 B:HIS109 4.1 31.7 1.0
CH2 B:TRP107 4.2 33.9 1.0
CD2 B:HIS403 4.3 38.0 1.0
NE2 B:HIS403 4.5 36.6 1.0
CU B:CU602 4.5 61.0 1.0
NE2 B:HIS64 4.6 32.4 1.0
CA B:HIS66 4.7 32.2 1.0
OG B:SER241 4.7 38.3 1.0
CD2 B:TRP107 4.8 35.6 1.0
CD1 B:TRP107 4.9 35.3 1.0

Reference:

H.H.Ge, Y.X.Gao, Y.Z.Hong, M.Zhang, Y.Z.Xiao, M.K.Teng, L.W.Niu. Structure of Native Laccase B From Trametes Sp. AH28-2 Acta Crystallogr.,Sect.F V. 66 254 2010.
ISSN: ESSN 1744-3091
PubMed: 20208154
DOI: 10.1107/S1744309110000084
Page generated: Wed Jul 31 01:15:24 2024

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