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Copper in PDB 3pxl: Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta

Enzymatic activity of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta

All present enzymatic activity of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta:
1.10.3.2;

Protein crystallography data

The structure of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta, PDB code: 3pxl was solved by K.M.Polyakov, T.V.Fedorova, S.A.Kurzeev, A.N.Popov, V.S.Lamzin, O.V.Koroleva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.00 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.653, 77.051, 130.216, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 17.9

Copper Binding Sites:

The binding sites of Copper atom in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta (pdb code 3pxl). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta, PDB code: 3pxl:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 3pxl

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Copper binding site 1 out of 5 in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1500

b:15.0
occ:0.75
CU A:CU1500 0.0 15.0 0.8
CU A:CU1500 1.7 27.4 0.1
NE2 A:HIS400 2.0 14.8 1.0
NE2 A:HIS452 2.0 16.7 1.0
NE2 A:HIS111 2.0 14.7 1.0
O A:HOH1411 2.3 21.4 0.8
CE1 A:HIS400 2.8 14.8 1.0
CE1 A:HIS452 2.9 16.3 1.0
CE1 A:HIS111 2.9 14.8 1.0
HE1 A:HIS400 3.0 14.7 1.0
CD2 A:HIS452 3.0 15.2 1.0
CD2 A:HIS400 3.1 13.5 1.0
CD2 A:HIS111 3.1 13.6 1.0
HE1 A:HIS111 3.1 14.9 1.0
HE1 A:HIS452 3.1 15.7 1.0
HD2 A:HIS452 3.2 15.4 1.0
HD2 A:PHE450 3.3 14.8 1.0
HD2 A:HIS111 3.3 13.6 1.0
HD2 A:HIS400 3.4 13.5 1.0
HB3 A:PHE450 3.6 13.9 1.0
HG3 A:PRO79 3.7 14.5 1.0
ND1 A:HIS398 3.8 15.7 0.8
O A:HOH867 3.8 26.4 1.0
ND1 A:HIS400 4.0 14.9 1.0
ND1 A:HIS452 4.0 14.8 1.0
CD2 A:PHE450 4.1 14.6 1.0
ND1 A:HIS111 4.1 15.5 1.0
CG A:HIS452 4.1 15.7 1.0
CD2 A:HIS398 4.1 15.6 0.2
CG A:HIS400 4.1 13.3 1.0
CG A:HIS111 4.2 13.7 1.0
CE1 A:HIS398 4.4 13.3 0.8
HE1 A:HIS109 4.4 15.2 1.0
HG2 A:PRO79 4.4 14.6 1.0
HD2 A:HIS64 4.4 15.8 1.0
CB A:PHE450 4.4 13.5 1.0
CG A:PRO79 4.5 14.5 1.0
CU A:CU1502 4.5 17.7 0.2
HD21 A:LEU459 4.5 17.1 0.0
HB2 A:PHE450 4.5 13.9 1.0
CD2 A:HIS64 4.6 15.9 1.0
CG A:PHE450 4.7 13.8 1.0
NE2 A:HIS64 4.7 17.0 1.0
HD1 A:HIS400 4.7 14.3 1.0
HD2 A:HIS454 4.7 16.0 1.0
HE2 A:PHE450 4.8 15.6 1.0
HD1 A:HIS452 4.8 15.0 1.0
HD1 A:HIS111 4.8 14.9 1.0
HB3 A:PRO79 4.9 14.4 1.0
CE2 A:PHE450 4.9 16.4 1.0
CG A:HIS398 4.9 14.9 0.8
HD22 A:LEU459 5.0 17.1 0.0
CD2 A:HIS454 5.0 16.0 1.0
CG A:HIS398 5.0 15.1 0.2

Copper binding site 2 out of 5 in 3pxl

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Copper binding site 2 out of 5 in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1500

b:27.4
occ:0.15
CU A:CU1500 0.0 27.4 0.1
CU A:CU1500 1.7 15.0 0.8
O A:HOH1411 1.8 21.4 0.8
ND1 A:HIS398 2.1 15.7 0.8
NE2 A:HIS400 2.3 14.8 1.0
NE2 A:HIS452 2.3 16.7 1.0
CD2 A:HIS398 2.6 15.6 0.2
CD2 A:HIS400 2.9 13.5 1.0
HD2 A:HIS400 2.9 13.5 1.0
CE1 A:HIS452 3.0 16.3 1.0
CE1 A:HIS398 3.0 13.3 0.8
HE1 A:HIS452 3.0 15.7 1.0
CG A:HIS398 3.2 14.9 0.8
CD2 A:HIS452 3.3 15.2 1.0
HD2 A:HIS454 3.3 16.0 1.0
CG A:HIS398 3.3 15.1 0.2
CE1 A:HIS400 3.4 14.8 1.0
NE2 A:HIS111 3.5 14.7 1.0
CU A:CU1502 3.6 17.7 0.2
HD2 A:HIS452 3.6 15.4 1.0
NE2 A:HIS398 3.7 14.7 0.2
CB A:HIS398 3.7 15.4 1.0
HE1 A:HIS400 3.7 14.7 1.0
CD2 A:HIS454 3.8 16.0 1.0
ND1 A:HIS452 4.1 14.8 1.0
NE2 A:HIS454 4.1 15.5 1.0
CG A:HIS400 4.1 13.3 1.0
NE2 A:HIS398 4.2 19.4 0.8
O A:HOH867 4.2 26.4 1.0
HD2 A:HIS64 4.2 15.8 1.0
HD2 A:HIS111 4.3 13.6 1.0
CD2 A:HIS398 4.3 14.8 0.8
CG A:HIS452 4.3 15.7 1.0
ND1 A:HIS400 4.3 14.9 1.0
CD2 A:HIS111 4.3 13.6 1.0
HB3 A:PHE450 4.4 13.9 1.0
NE2 A:HIS64 4.4 17.0 1.0
CU A:CU1501 4.4 16.1 0.8
CD2 A:HIS64 4.5 15.9 1.0
HE1 A:HIS66 4.5 15.2 1.0
ND1 A:HIS398 4.5 14.7 0.2
CE1 A:HIS111 4.5 14.8 1.0
O A:HIS398 4.6 13.7 1.0
HE1 A:HIS109 4.6 15.2 1.0
CE1 A:HIS398 4.7 13.2 0.2
HE1 A:HIS111 4.7 14.9 1.0
HD2 A:PHE450 4.8 14.8 1.0
HD1 A:HIS452 4.8 15.0 1.0
CG A:HIS454 4.8 15.9 1.0
ND1 A:HIS66 4.9 15.7 1.0
C A:HIS398 4.9 13.8 1.0
CE1 A:HIS66 4.9 15.4 1.0
CA A:HIS398 4.9 14.4 1.0

Copper binding site 3 out of 5 in 3pxl

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Copper binding site 3 out of 5 in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1501

b:16.1
occ:0.80
ND1 A:HIS66 2.0 15.7 1.0
NE2 A:HIS109 2.0 15.9 1.0
NE2 A:HIS454 2.1 15.5 1.0
HD2 A:HIS64 2.8 15.8 1.0
CE1 A:HIS66 2.9 15.4 1.0
HB2 A:HIS66 2.9 13.3 1.0
O A:HOH1411 3.0 21.4 0.8
CE1 A:HIS109 3.0 15.7 1.0
CE1 A:HIS454 3.0 15.6 1.0
CD2 A:HIS109 3.0 15.1 1.0
HE1 A:HIS66 3.0 15.2 1.0
CG A:HIS66 3.0 13.6 1.0
HE1 A:HIS454 3.1 15.2 1.0
HE1 A:HIS109 3.2 15.2 1.0
CD2 A:HIS454 3.2 16.0 1.0
HD2 A:HIS109 3.2 14.9 1.0
HZ2 A:TRP107 3.3 13.7 1.0
HD2 A:HIS454 3.4 16.0 1.0
CB A:HIS66 3.5 13.7 1.0
CZ2 A:TRP107 3.6 14.1 1.0
CD2 A:HIS64 3.7 15.9 1.0
HB2 A:ALA241 3.7 14.6 0.0
HE1 A:TRP107 3.8 13.9 1.0
CE2 A:TRP107 3.8 13.1 1.0
NE1 A:TRP107 4.0 14.6 1.0
HB1 A:ALA241 4.0 14.6 0.0
NE2 A:HIS66 4.0 15.9 1.0
HB3 A:HIS66 4.0 13.3 1.0
ND1 A:HIS109 4.1 14.8 1.0
CU A:CU1502 4.1 17.7 0.2
CD2 A:HIS66 4.1 15.6 1.0
CG A:HIS109 4.1 14.4 1.0
ND1 A:HIS454 4.1 14.3 1.0
NE2 A:HIS64 4.2 17.0 1.0
ND1 A:HIS398 4.2 15.7 0.8
CE1 A:HIS398 4.3 13.3 0.8
CG A:HIS454 4.3 15.9 1.0
CB A:ALA241 4.3 14.2 1.0
CH2 A:TRP107 4.3 13.8 1.0
CU A:CU1500 4.4 27.4 0.1
HA A:HIS66 4.4 13.7 1.0
O A:HOH867 4.5 26.4 1.0
HH2 A:TRP107 4.5 13.8 1.0
CA A:HIS66 4.6 13.3 1.0
HD2 A:HIS111 4.7 13.6 1.0
CD2 A:TRP107 4.7 13.9 1.0
HE2 A:HIS66 4.8 15.8 1.0
CG A:HIS64 4.9 15.4 1.0
HD1 A:HIS109 4.9 14.6 1.0
CD1 A:TRP107 4.9 13.8 1.0
CD2 A:HIS398 4.9 15.6 0.2
HD1 A:HIS454 4.9 14.6 1.0
HB3 A:ALA241 4.9 14.6 0.0
HB3 A:HIS64 4.9 13.6 1.0
HD2 A:HIS66 5.0 15.3 1.0

Copper binding site 4 out of 5 in 3pxl

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Copper binding site 4 out of 5 in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1503

b:14.6
occ:0.80
ND1 A:HIS458 2.0 17.9 1.0
ND1 A:HIS395 2.0 14.8 1.0
SG A:CYS453 2.2 16.5 1.0
HD13 A:ILE455 2.7 17.4 0.0
CE1 A:HIS458 3.0 15.9 1.0
CE1 A:HIS395 3.0 16.1 1.0
HB A:ILE455 3.0 14.7 1.0
CG A:HIS458 3.0 15.1 1.0
HD2 A:PHE463 3.0 14.6 1.0
HB3 A:HIS395 3.1 15.2 1.0
CG A:HIS395 3.1 15.3 1.0
HE1 A:HIS458 3.1 16.2 1.0
HE1 A:HIS395 3.1 16.3 1.0
HB2 A:HIS458 3.2 14.9 1.0
HG A:CYS453 3.3 15.8 1.0
CB A:CYS453 3.3 13.9 1.0
HB3 A:HIS458 3.3 14.9 1.0
HA A:HIS395 3.3 15.3 1.0
HE2 A:PHE463 3.3 14.9 1.0
HB2 A:CYS453 3.4 14.2 1.0
CB A:HIS458 3.4 15.1 1.0
HB3 A:CYS453 3.4 14.2 1.0
CB A:HIS395 3.5 14.7 1.0
CD1 A:ILE455 3.6 17.3 1.0
CD2 A:PHE463 3.8 14.7 1.0
HD2 A:PRO396 3.8 14.6 1.0
CB A:ILE455 3.9 14.6 1.0
CE2 A:PHE463 3.9 15.2 1.0
HD12 A:ILE455 3.9 17.4 0.0
CA A:HIS395 3.9 15.4 1.0
CG1 A:ILE455 4.0 15.1 1.0
HG13 A:ILE455 4.1 15.1 1.0
H A:ILE455 4.1 15.1 1.0
NE2 A:HIS458 4.1 16.0 1.0
NE2 A:HIS395 4.1 17.8 1.0
CD2 A:HIS458 4.2 15.3 1.0
CD2 A:HIS395 4.2 17.1 1.0
HD11 A:ILE455 4.2 17.4 0.0
HG22 A:ILE455 4.4 15.0 0.0
HB2 A:HIS395 4.4 15.1 1.0
O A:GLY392 4.6 22.3 1.0
CG2 A:ILE455 4.6 15.2 1.0
CA A:CYS453 4.6 14.2 1.0
CD A:PRO396 4.7 15.2 1.0
N A:ILE455 4.8 14.6 1.0
HA A:CYS453 4.8 14.0 1.0
HG21 A:ILE455 4.8 15.0 0.0
HD3 A:PRO396 4.8 14.4 1.0
HE2 A:HIS458 4.9 15.8 1.0
HE2 A:HIS395 4.9 17.0 1.0
CA A:ILE455 4.9 14.8 1.0
CA A:HIS458 4.9 15.0 1.0
HE1 A:PHE397 4.9 15.9 1.0
C A:HIS395 4.9 15.4 1.0
N A:HIS395 5.0 15.7 1.0
HZ A:PHE337 5.0 17.8 1.0
O A:ILE455 5.0 14.9 1.0
HG12 A:ILE455 5.0 15.4 1.0

Copper binding site 5 out of 5 in 3pxl

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Copper binding site 5 out of 5 in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1502

b:17.7
occ:0.20
CE1 A:HIS398 1.4 13.3 0.8
NE2 A:HIS64 1.9 17.0 1.0
NE2 A:HIS398 2.0 14.7 0.2
NE2 A:HIS398 2.3 19.4 0.8
ND1 A:HIS398 2.6 15.7 0.8
CD2 A:HIS398 2.6 15.6 0.2
O A:HOH1003 2.6 17.4 1.0
CE1 A:HIS64 2.8 15.6 1.0
CD2 A:HIS64 2.9 15.9 1.0
CE1 A:HIS398 2.9 13.2 0.2
HE1 A:HIS64 3.0 16.0 1.0
HA A:HIS66 3.0 13.7 1.0
HD2 A:HIS64 3.1 15.8 1.0
ND1 A:HIS66 3.3 15.7 1.0
H A:GLY67 3.4 14.2 1.0
NE2 A:HIS400 3.5 14.8 1.0
CE1 A:HIS400 3.5 14.8 1.0
CD2 A:HIS398 3.5 14.8 0.8
CU A:CU1500 3.6 27.4 0.1
CG A:HIS66 3.6 13.6 1.0
CG A:HIS398 3.6 14.9 0.8
CE1 A:HIS66 3.7 15.4 1.0
CD2 A:HIS400 3.7 13.5 1.0
CG A:HIS398 3.7 15.1 0.2
ND1 A:HIS400 3.7 14.9 1.0
O A:HOH1411 3.7 21.4 0.8
HA A:HIS400 3.8 13.3 1.0
HE1 A:HIS400 3.8 14.7 1.0
CG A:HIS400 3.8 13.3 1.0
ND1 A:HIS398 3.8 14.7 0.2
ND1 A:HIS64 3.9 16.0 1.0
CA A:HIS66 3.9 13.3 1.0
HE1 A:HIS66 4.0 15.2 1.0
CG A:HIS64 4.0 15.4 1.0
NE2 A:HIS66 4.0 15.9 1.0
CD2 A:HIS66 4.0 15.6 1.0
N A:GLY67 4.1 14.2 1.0
CU A:CU1501 4.1 16.1 0.8
HD2 A:HIS400 4.1 13.5 1.0
HD1 A:HIS400 4.1 14.3 1.0
CB A:HIS66 4.1 13.7 1.0
HB2 A:HIS66 4.2 13.3 1.0
C A:HIS66 4.5 13.9 1.0
CU A:CU1500 4.5 15.0 0.8
O A:HOH1038 4.5 15.5 1.0
HE2 A:HIS66 4.6 15.8 1.0
CA A:HIS400 4.6 13.3 1.0
HD2 A:HIS66 4.6 15.3 1.0
HD1 A:HIS64 4.7 15.6 1.0
O A:HOH1089 4.7 19.6 1.0
CB A:HIS400 4.7 13.6 1.0
HA2 A:GLY67 4.9 14.6 1.0
HD2 A:HIS454 4.9 16.0 1.0
HB3 A:HIS400 4.9 13.2 1.0
N A:HIS66 5.0 14.4 1.0

Reference:

K.M.Polyakov, T.V.Fedorova, S.A.Kurzeev, A.N.Popov, V.S.Lamzin, O.V.Koroleva. Crystal Structure of T2-Depleted Fungal Laccase From Trametes Hirsuta at Low and High Dose of Ionization Radiation. To Be Published.
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