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Copper in the structure of Crystal Structure of Laccase From Coriolopsis Gallica (pdb 2vds)

The binding sites of Copper atom in the structure of Crystal Structure of Laccase From Coriolopsis Gallica (pdb code 2vds). This binding sites where shown with 5.0 Angstroms radius around Copper atom.
The 2vds 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)76.7-2.3
Space groupP212121
a (A)56.376
b (A)86.795
c (A)153.573
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)18.4
Rfree (%)22.4

Copper Binding Sites:

Copper binding site 1 out of 4 in 2vds


Copper binding site 1 out of 4 in 2vds
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stereopicture of Copper binding site 1 out of 4 in 2vds
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2vds. 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: His396, A: His398, A: Phe446, A: His448, A: His450, A: Cu3517, A: Cu519, A: Hoh2381,

conact list:


AtomAtomDistance (A)
CuNE2 A:His644.58
CuCD2 A:His644.37
CuCG A:His644.98
CuCG A:Pro794.68
CuNE2 A:His1112.01
CuND1 A:His1114.07
CuCD2 A:His1113.07
CuCE1 A:His1112.93
CuCG A:His1114.17
CuNE2 A:His3964.74
CuCD2 A:His3963.88
CuCG A:His3964.87
CuNE2 A:His3982.11
CuND1 A:His3984.05
CuCD2 A:His3983.29
CuCE1 A:His3982.84
CuCG A:His3984.29
CuCB A:Phe4464.54
CuCD2 A:Phe4464.35
CuCG A:Phe4464.86
CuNE2 A:His4481.96
CuND1 A:His4483.94
CuCD2 A:His4483.11
CuCE1 A:His4482.76
CuCG A:His4484.13
CuNE2 A:His4504.55
CuCD2 A:His4504.74
CuCU A:Cu35174.70
CuCU A:Cu5194.57
CuO A:Hoh23814.63

interactive model:


Copper binding site 2 out of 4 in 2vds


Copper binding site 2 out of 4 in 2vds
Click to enlarge
stereopicture of Copper binding site 2 out of 4 in 2vds
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2vds. 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: His396, A: His450, A: Cu3516, A: Cu519,

conact list:


AtomAtomDistance (A)
CuNE2 A:His644.02
CuCD2 A:His643.61
CuCG A:His644.88
CuNE2 A:His664.08
CuCB A:His663.73
CuND1 A:His662.09
CuCD2 A:His664.27
CuCE1 A:His662.89
CuCG A:His663.24
CuCA A:His664.82
CuCZ2 A:Trp1073.77
CuCE2 A:Trp1074.15
CuNE1 A:Trp1074.28
CuCH2 A:Trp1074.49
CuNE2 A:His1092.39
CuND1 A:His1094.41
CuCD2 A:His1093.39
CuCE1 A:His1093.28
CuCG A:His1094.50
CuCB A:Ala2404.26
CuNE2 A:His3964.31
CuCD2 A:His3964.12
CuCG A:His3964.86
CuNE2 A:His4502.13
CuND1 A:His4504.05
CuCD2 A:His4503.28
CuCE1 A:His4502.86
CuCG A:His4504.28
CuCU A:Cu35164.70
CuCU A:Cu5193.86

interactive model:


Copper binding site 3 out of 4 in 2vds


Copper binding site 3 out of 4 in 2vds
Click to enlarge
stereopicture of Copper binding site 3 out of 4 in 2vds
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2vds. 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: Gly390, A: His393, A: Pro394, A: Cys449, A: Ile451, A: His454, A: Phe459,

conact list:


AtomAtomDistance (A)
CuO A:Gly3904.92
CuNE2 A:His3934.38
CuN A:His3934.85
CuCB A:His3933.29
CuND1 A:His3932.35
CuCD2 A:His3934.29
CuC A:His3934.76
CuCE1 A:His3933.37
CuCG A:His3933.14
CuCA A:His3933.81
CuN A:Pro3944.95
CuCD A:Pro3944.57
CuCB A:Cys4493.37
CuSG A:Cys4492.12
CuCA A:Cys4494.69
CuO A:Ile4514.79
CuN A:Ile4514.67
CuCB A:Ile4513.76
CuCD1 A:Ile4513.42
CuCG2 A:Ile4514.59
CuCG1 A:Ile4514.02
CuCA A:Ile4514.75
CuNE2 A:His4544.60
CuCB A:His4543.57
CuND1 A:His4542.49
CuCD2 A:His4544.59
CuCE1 A:His4543.49
CuCG A:His4543.41
CuCD1 A:Phe4593.75
CuCE1 A:Phe4594.03
CuCG A:Phe4594.99

interactive model:


Copper binding site 4 out of 4 in 2vds


Copper binding site 4 out of 4 in 2vds
Click to enlarge
stereopicture of Copper binding site 4 out of 4 in 2vds
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2vds. 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: Trp65, A: His66, A: Gly67, A: His396, A: His398, A: Cu3516, A: Cu3517, A: Hoh2073, A: Hoh2075, A: Hoh2344,

conact list:


AtomAtomDistance (A)
CuNE2 A:His641.78
CuND1 A:His643.79
CuCD2 A:His642.90
CuCE1 A:His642.64
CuCG A:His643.95
CuO A:Trp654.97
CuNE2 A:His664.03
CuN A:His664.76
CuCB A:His663.96
CuND1 A:His663.28
CuCD2 A:His663.95
CuC A:His664.45
CuCE1 A:His663.64
CuCG A:His663.51
CuCA A:His663.77
CuN A:Gly674.13
CuNE2 A:His3961.83
CuND1 A:His3963.92
CuCD2 A:His3962.72
CuCE1 A:His3962.89
CuCG A:His3963.88
CuNE2 A:His3983.57
CuCB A:His3984.90
CuND1 A:His3983.73
CuCD2 A:His3983.89
CuCE1 A:His3983.49
CuCG A:His3983.98
CuCA A:His3984.84
CuCU A:Cu35164.57
CuCU A:Cu35173.86
CuO A:Hoh20732.77
CuO A:Hoh20754.66
CuO A:Hoh23444.99

interactive model:




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