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Copper in the structure of Crystal Structure of A Coriolopsis Gallica Laccase At 1.7 A Resolution (pdb 2vdz)

The binding sites of Copper atom in the structure of Crystal Structure of A Coriolopsis Gallica Laccase At 1.7 A Resolution (pdb code 2vdz). This binding sites where shown with 5.0 Angstroms radius around Copper atom.
The 2vdz structure was solved by E.DE LA MORA, B.VALDERRAMA, E.HORJALES, E.RUDINO-PINERA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)76.2-1.7
Space groupP212121
a (A)56.382
b (A)86.128
c (A)152.645
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)14.6
Rfree (%)16.7

Copper Binding Sites:

Copper binding site 1 out of 4 in 2vdz


Copper binding site 1 out of 4 in 2vdz
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stereopicture of Copper binding site 1 out of 4 in 2vdz
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2vdz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His64, A: His66, A: Trp107, A: His109, A: Ala240, A: His397, A: His451, A: Cu1499, A: Hoh2612, A: Hoh2662,

conact list:


AtomAtomDistance (A)
CuNE2 A:His644.20
CuCD2 A:His643.66
CuCG A:His644.87
CuNE2 A:His664.08
CuCB A:His663.48
CuND1 A:His662.03
CuCD2 A:His664.17
CuCE1 A:His662.94
CuCG A:His663.08
CuCA A:His664.62
CuCD2 A:Trp1074.87
CuCZ2 A:Trp1073.59
CuCE2 A:Trp1073.91
CuNE1 A:Trp1074.06
CuCH2 A:Trp1074.33
CuNE2 A:His1092.22
CuND1 A:His1094.31
CuCD2 A:His1093.15
CuCE1 A:His1093.23
CuCG A:His1094.31
CuCB A:Ala2404.27
CuNE2 A:His3974.51
CuNE2 A:His3974.30
CuCD2 A:His3974.37
CuCD2 A:His3974.67
CuCE1 A:His3974.66
CuNE2 A:His4512.20
CuND1 A:His4514.27
CuCD2 A:His4513.22
CuCE1 A:His4513.13
CuCG A:His4514.34
CuCU A:Cu14993.97
CuO A:Hoh26122.75
CuO A:Hoh26624.37

interactive model:


Copper binding site 2 out of 4 in 2vdz


Copper binding site 2 out of 4 in 2vdz
Click to enlarge
stereopicture of Copper binding site 2 out of 4 in 2vdz
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2vdz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His64, A: Pro79, A: His111, A: His397, A: His399, A: Phe447, A: His449, A: His451, A: Cu1499, A: Hoh2612, A: Hoh2662,

conact list:


AtomAtomDistance (A)
CuNE2 A:His644.78
CuCD2 A:His644.54
CuCG A:Pro794.67
CuNE2 A:His1112.06
CuND1 A:His1114.14
CuCD2 A:His1113.08
CuCE1 A:His1113.01
CuCG A:His1114.20
CuNE2 A:His3974.77
CuNE2 A:His3972.52
CuND1 A:His3974.26
CuCD2 A:His3973.99
CuCD2 A:His3973.78
CuCE1 A:His3972.99
CuCG A:His3974.66
CuNE2 A:His3992.07
CuND1 A:His3994.07
CuCD2 A:His3993.19
CuCE1 A:His3992.89
CuCG A:His3994.24
CuCB A:Phe4474.43
CuCD2 A:Phe4474.24
CuCG A:Phe4474.75
CuNE2 A:His4492.04
CuND1 A:His4494.12
CuCD2 A:His4493.08
CuCE1 A:His4492.99
CuCG A:His4494.19
CuNE2 A:His4514.97
CuCD2 A:His4514.97
CuCU A:Cu14994.39
CuO A:Hoh26122.28
CuO A:Hoh26623.73

interactive model:


Copper binding site 3 out of 4 in 2vdz


Copper binding site 3 out of 4 in 2vdz
Click to enlarge
stereopicture of Copper binding site 3 out of 4 in 2vdz
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2vdz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: His64, A: His66, A: Gly67, A: His397, A: His399, A: Cu1497, A: Cu1498, A: Hoh2149, A: Hoh2164, A: Hoh2612, A: Hoh2614,

conact list:


AtomAtomDistance (A)
CuNE2 A:His641.78
CuND1 A:His643.82
CuCD2 A:His642.77
CuCE1 A:His642.75
CuCG A:His643.87
CuNE2 A:His664.18
CuCB A:His664.20
CuND1 A:His663.35
CuCD2 A:His664.21
CuC A:His664.67
CuCE1 A:His663.70
CuCG A:His663.71
CuCA A:His664.02
CuN A:Gly674.28
CuNE2 A:His3971.87
CuNE2 A:His3973.55
CuND1 A:His3973.98
CuCD2 A:His3972.70
CuCD2 A:His3973.35
CuCE1 A:His3972.97
CuCE1 A:His3974.80
CuCG A:His3973.90
CuCG A:His3974.58
CuNE2 A:His3993.33
CuCB A:His3994.72
CuND1 A:His3993.64
CuCD2 A:His3993.60
CuCE1 A:His3993.38
CuCG A:His3993.79
CuCA A:His3994.62
CuCU A:Cu14973.97
CuCU A:Cu14984.39
CuO A:Hoh21492.80
CuO A:Hoh21644.64
CuO A:Hoh26123.54
CuO A:Hoh26144.94

interactive model:


Copper binding site 4 out of 4 in 2vdz


Copper binding site 4 out of 4 in 2vdz
Click to enlarge
stereopicture of Copper binding site 4 out of 4 in 2vdz
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2vdz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Gly391, A: His394, A: Pro395, A: Cys450, A: Ile452, A: His455, A: Phe460,

conact list:


AtomAtomDistance (A)
CuO A:Gly3914.67
CuNE2 A:His3944.14
CuN A:His3944.99
CuCB A:His3943.43
CuND1 A:His3942.10
CuCD2 A:His3944.18
CuC A:His3944.92
CuCE1 A:His3943.03
CuCG A:His3943.08
CuCA A:His3943.96
CuCD A:Pro3954.70
CuCB A:Cys4503.34
CuSG A:Cys4502.22
CuCA A:Cys4504.69
CuO A:Ile4524.88
CuN A:Ile4524.79
CuCB A:Ile4523.82
CuCD1 A:Ile4523.48
CuCG2 A:Ile4524.67
CuCG1 A:Ile4523.98
CuCA A:Ile4524.85
CuNE2 A:His4554.22
CuCB A:His4553.35
CuND1 A:His4552.11
CuCD2 A:His4554.22
CuCE1 A:His4553.11
CuCG A:His4553.08
CuCA A:His4554.88
CuCD1 A:Phe4603.71
CuCE1 A:Phe4603.92
CuCG A:Phe4604.98

interactive model:




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