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Copper in PDB 3v9c: Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta at Low Dose of Ionization Radiation

Enzymatic activity of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta at Low Dose of Ionization Radiation

All present enzymatic activity of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta at Low Dose of Ionization Radiation:
1.10.3.2;

Protein crystallography data

The structure of Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta at Low Dose of Ionization Radiation, PDB code: 3v9c 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 / 2.00
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 (%) 16.1 / 20

Copper Binding Sites:

The binding sites of Copper atom in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta at Low Dose of Ionization Radiation (pdb code 3v9c). 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 at Low Dose of Ionization Radiation, PDB code: 3v9c:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 3v9c

Go back to Copper Binding Sites List in 3v9c
Copper binding site 1 out of 5 in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta at Low Dose of Ionization Radiation


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 at Low Dose of Ionization Radiation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1500

b:26.9
occ:0.70
 CU A:CU1500 0.0 26.9 0.7
CU A:CU1500 1.1 23.6 0.2
O2 A:OXY1000 1.9 28.7 0.8
NE2 A:HIS452 2.0 24.0 1.0
NE2 A:HIS400 2.0 23.2 1.0
NE2 A:HIS111 2.0 21.3 1.0
O1 A:OXY1000 2.0 28.8 0.8
CE1 A:HIS400 2.7 22.4 1.0
CE1 A:HIS452 2.8 24.7 1.0
CD2 A:HIS111 2.9 20.8 1.0
CE1 A:HIS111 3.1 20.3 1.0
CD2 A:HIS452 3.1 21.1 1.0
CD2 A:HIS400 3.2 20.6 1.0
ND1 A:HIS398 3.3 24.4 0.8
CE1 A:HIS398 3.9 25.2 0.8
CU A:CU1502 3.9 25.6 0.2
CD2 A:HIS398 3.9 23.7 0.2
ND1 A:HIS400 3.9 21.3 1.0
ND1 A:HIS452 4.0 24.2 1.0
CU A:CU1501 4.0 29.6 0.8
CG A:HIS111 4.1 20.3 1.0
ND1 A:HIS111 4.2 20.8 1.0
CD2 A:HIS64 4.2 22.6 1.0
CG A:HIS452 4.2 22.2 1.0
CG A:HIS400 4.2 21.0 1.0
NE2 A:HIS64 4.3 24.3 1.0
NE2 A:HIS454 4.3 25.7 1.0
CD2 A:HIS454 4.4 24.7 1.0
CG A:HIS398 4.5 23.7 0.8
CE1 A:HIS109 4.6 18.6 1.0
CG A:HIS398 4.8 23.2 0.2
CD2 A:PHE450 4.8 19.9 1.0
CG A:HIS64 4.8 20.5 1.0
CG A:PRO79 4.8 19.4 1.0
NE2 A:HIS398 4.8 24.8 0.2
CB A:HIS398 5.0 22.6 1.0

Copper binding site 2 out of 5 in 3v9c

Go back to Copper Binding Sites List in 3v9c
Copper binding site 2 out of 5 in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta at Low Dose of Ionization Radiation


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 at Low Dose of Ionization Radiation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1500

b:23.6
occ:0.20
 CU A:CU1500 0.0 23.6 0.2
CU A:CU1500 1.1 26.9 0.7
O1 A:OXY1000 1.9 28.8 0.8
O2 A:OXY1000 2.0 28.7 0.8
NE2 A:HIS452 2.0 24.0 1.0
NE2 A:HIS400 2.0 23.2 1.0
ND1 A:HIS398 2.2 24.4 0.8
CD2 A:HIS398 2.8 23.7 0.2
CE1 A:HIS452 2.8 24.7 1.0
CD2 A:HIS400 2.9 20.6 1.0
CE1 A:HIS398 2.9 25.2 0.8
CE1 A:HIS400 3.0 22.4 1.0
CD2 A:HIS452 3.1 21.1 1.0
NE2 A:HIS111 3.2 21.3 1.0
CU A:CU1502 3.3 25.6 0.2
CG A:HIS398 3.4 23.7 0.8
CG A:HIS398 3.6 23.2 0.2
CU A:CU1501 3.8 29.6 0.8
CD2 A:HIS454 3.8 24.7 1.0
NE2 A:HIS398 3.9 24.8 0.2
CB A:HIS398 3.9 22.6 1.0
NE2 A:HIS454 4.0 25.7 1.0
ND1 A:HIS452 4.0 24.2 1.0
CD2 A:HIS111 4.0 20.8 1.0
CG A:HIS400 4.0 21.0 1.0
ND1 A:HIS400 4.0 21.3 1.0
CG A:HIS452 4.1 22.2 1.0
NE2 A:HIS398 4.2 27.5 0.8
CE1 A:HIS111 4.2 20.3 1.0
NE2 A:HIS64 4.2 24.3 1.0
CD2 A:HIS64 4.3 22.6 1.0
CD2 A:HIS398 4.4 25.4 0.8
ND1 A:HIS66 4.7 25.2 1.0
CE1 A:HIS66 4.8 25.2 1.0
ND1 A:HIS398 4.9 23.8 0.2
CG A:HIS454 4.9 23.8 1.0
O A:HIS398 4.9 21.3 1.0
CE1 A:HIS398 5.0 24.3 0.2

Copper binding site 3 out of 5 in 3v9c

Go back to Copper Binding Sites List in 3v9c
Copper binding site 3 out of 5 in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta at Low Dose of Ionization Radiation


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 at Low Dose of Ionization Radiation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1501

b:29.6
occ:0.80
 NE2 A:HIS454 2.0 25.7 1.0
O1 A:OXY1000 2.0 28.8 0.8
ND1 A:HIS66 2.0 25.2 1.0
NE2 A:HIS109 2.0 23.4 1.0
O2 A:OXY1000 2.6 28.7 0.8
CE1 A:HIS109 2.8 18.6 1.0
CE1 A:HIS66 2.8 25.2 1.0
CE1 A:HIS454 2.9 24.5 1.0
CD2 A:HIS454 3.1 24.7 1.0
CG A:HIS66 3.2 20.7 1.0
CD2 A:HIS109 3.2 19.4 1.0
CU A:CU1502 3.5 25.6 0.2
CD2 A:HIS64 3.5 22.6 1.0
CB A:HIS66 3.6 19.6 1.0
CU A:CU1500 3.8 23.6 0.2
ND1 A:HIS398 3.9 24.4 0.8
CZ2 A:TRP107 3.9 17.3 1.0
CE1 A:HIS398 4.0 25.2 0.8
ND1 A:HIS109 4.0 21.9 1.0
NE2 A:HIS66 4.0 24.7 1.0
CU A:CU1500 4.0 26.9 0.7
NE2 A:HIS64 4.0 24.3 1.0
ND1 A:HIS454 4.1 23.2 1.0
CD2 A:HIS398 4.2 23.7 0.2
CG A:HIS454 4.2 23.8 1.0
CD2 A:HIS66 4.2 21.6 1.0
CG A:HIS109 4.2 19.8 1.0
CE2 A:TRP107 4.3 18.8 1.0
NE1 A:TRP107 4.4 18.1 1.0
NE2 A:HIS398 4.6 24.8 0.2
CB A:ALA241 4.6 18.8 1.0
CH2 A:TRP107 4.7 16.9 1.0
CG A:HIS64 4.7 20.5 1.0
CA A:HIS66 4.7 19.3 1.0
CG A:HIS398 4.8 23.7 0.8
CD2 A:HIS111 4.9 20.8 1.0
CG A:HIS398 4.9 23.2 0.2
NE2 A:HIS398 4.9 27.5 0.8

Copper binding site 4 out of 5 in 3v9c

Go back to Copper Binding Sites List in 3v9c
Copper binding site 4 out of 5 in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta at Low Dose of Ionization Radiation


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 at Low Dose of Ionization Radiation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1503

b:22.1
occ:0.80
 ND1 A:HIS395 2.0 23.2 1.0
ND1 A:HIS458 2.0 21.0 1.0
SG A:CYS453 2.2 22.8 1.0
CE1 A:HIS395 2.8 23.8 1.0
CE1 A:HIS458 3.0 24.0 1.0
CG A:HIS458 3.0 21.5 1.0
CG A:HIS395 3.1 23.5 1.0
CB A:CYS453 3.3 20.4 1.0
CB A:HIS458 3.3 21.6 1.0
CB A:HIS395 3.6 22.6 1.0
CD2 A:PHE463 3.6 21.0 1.0
CD1 A:ILE455 3.7 19.5 1.0
CE2 A:PHE463 3.8 21.5 1.0
CB A:ILE455 3.9 21.5 1.0
NE2 A:HIS395 4.0 24.4 1.0
CA A:HIS395 4.0 23.2 1.0
NE2 A:HIS458 4.1 22.4 1.0
CD2 A:HIS458 4.1 21.1 1.0
CD2 A:HIS395 4.1 22.5 1.0
CG1 A:ILE455 4.3 20.3 1.0
O A:GLY392 4.4 32.0 1.0
CA A:CYS453 4.7 21.0 1.0
CG2 A:ILE455 4.7 20.4 1.0
CD A:PRO396 4.7 21.2 1.0
N A:ILE455 4.8 22.6 1.0
CA A:HIS458 4.9 22.2 1.0
CG A:PHE463 4.9 19.5 1.0
CA A:ILE455 4.9 22.1 1.0
O A:ILE455 5.0 22.4 1.0
CZ A:PHE337 5.0 23.3 1.0
C A:HIS395 5.0 22.4 1.0

Copper binding site 5 out of 5 in 3v9c

Go back to Copper Binding Sites List in 3v9c
Copper binding site 5 out of 5 in the Type-2 Cu-Depleted Fungus Laccase From Trametes Hirsuta at Low Dose of Ionization Radiation


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 at Low Dose of Ionization Radiation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1502

b:25.6
occ:0.20
 CE1 A:HIS398 1.4 25.2 0.8
NE2 A:HIS64 2.0 24.3 1.0
NE2 A:HIS398 2.0 24.8 0.2
NE2 A:HIS398 2.3 27.5 0.8
CD2 A:HIS398 2.3 23.7 0.2
ND1 A:HIS398 2.4 24.4 0.8
CD2 A:HIS64 2.8 22.6 1.0
O1 A:OXY1000 3.0 28.8 0.8
CE1 A:HIS64 3.0 22.6 1.0
ND1 A:HIS66 3.1 25.2 1.0
O A:HOH1003 3.2 22.9 1.0
CE1 A:HIS398 3.2 24.3 0.2
CU A:CU1500 3.3 23.6 0.2
CG A:HIS66 3.3 20.7 1.0
NE2 A:HIS400 3.4 23.2 1.0
CE1 A:HIS66 3.4 25.2 1.0
CD2 A:HIS398 3.5 25.4 0.8
CU A:CU1501 3.5 29.6 0.8
CG A:HIS398 3.5 23.7 0.8
CE1 A:HIS400 3.5 22.4 1.0
CG A:HIS398 3.6 23.2 0.2
CD2 A:HIS400 3.7 20.6 1.0
CD2 A:HIS66 3.8 21.6 1.0
CA A:HIS66 3.8 19.3 1.0
CU A:CU1500 3.9 26.9 0.7
NE2 A:HIS66 3.9 24.7 1.0
CB A:HIS66 3.9 19.6 1.0
ND1 A:HIS400 3.9 21.3 1.0
CG A:HIS64 4.0 20.5 1.0
O2 A:OXY1000 4.0 28.7 0.8
ND1 A:HIS398 4.0 23.8 0.2
CG A:HIS400 4.0 21.0 1.0
ND1 A:HIS64 4.0 20.3 1.0
N A:GLY67 4.2 19.1 1.0
C A:HIS66 4.5 19.3 1.0
O A:HOH1038 4.8 26.1 1.0
NE2 A:HIS454 4.8 25.7 1.0
CB A:HIS398 4.9 22.6 1.0
CA A:HIS400 4.9 20.0 1.0
NE2 A:HIS109 4.9 23.4 1.0
O A:HOH1028 4.9 22.3 1.0
N A:HIS66 5.0 19.0 1.0
CB A:HIS400 5.0 19.3 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 072 at Low and High Dose of Ionization Radiation To Be Published.
Page generated: Wed Jul 31 02:18:45 2024

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