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Zinc in the structure of Structures Of Spop-Substrate Complexes: Insights Into Architectures of Btb-CUL3 Ubiquitin Ligases: Spopmath- MACROH2ASBCPEP1 (pdb 3ivb)






The binding sites of Zinc atom in the structure of Structures Of Spop-Substrate Complexes: Insights Into Architectures of Btb-CUL3 Ubiquitin Ligases: Spopmath- MACROH2ASBCPEP1 (pdb code 3ivb). This binding sites where shown with 5.0 Angstroms radius around Zinc atom.
The 3ivb structure was solved by B.A.SCHULMAN, D.J.MILLER, M.F.CALABRESE, S.SEYEDIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)37.7-1.8
Space groupP6522
a (A)44.021
b (A)44.021
c (A)266.840
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)21.8
Rfree (%)24.7


Zinc Binding Sites:

Zinc binding site 1 out of 5 in 3ivb


Zinc binding site 1 out of 5 in 3ivb
Click to enlarge		stereopicture of Zinc binding site 1 out of 5 in 3ivb
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3ivb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Cys44, A: Glu46, A: Glu47, A: Zn4, A: Hoh217, A: Hoh226, A: Hoh240,

conact list:


AtomAtomDistance (A)
ZnCB A:Cys443.24
ZnSG A:Cys442.25
ZnCA A:Cys444.64
ZnCB A:Glu464.56
ZnC A:Glu464.94
ZnN A:Glu474.68
ZnOE1 A:Glu474.25
ZnCB A:Glu474.46
ZnOE2 A:Glu472.10
ZnCD A:Glu473.08
ZnCG A:Glu473.37
ZnZN A:Zn43.32
ZnO A:Hoh2172.75
ZnO A:Hoh2262.14
ZnO A:Hoh2404.64

interactive model:


Zinc binding site 2 out of 5 in 3ivb


Zinc binding site 2 out of 5 in 3ivb
Click to enlarge		stereopicture of Zinc binding site 2 out of 5 in 3ivb
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3ivb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Lys103, A: Glu113, A: Phe158, A: Glu160, A: Hoh169, A: Hoh237, A: Hoh238,

conact list:


AtomAtomDistance (A)
ZnCE A:Lys1034.58
ZnNZ A:Lys1034.18
ZnOE1 A:Glu1132.00
ZnOE2 A:Glu1132.70
ZnCD A:Glu1132.67
ZnCG A:Glu1134.12
ZnCE2 A:Phe1584.07
ZnCD2 A:Phe1584.48
ZnOE1 A:Glu1603.48
ZnOE2 A:Glu1602.52
ZnCD A:Glu1603.28
ZnCG A:Glu1604.56
ZnO A:Hoh1694.57
ZnO A:Hoh2371.75
ZnO A:Hoh2383.92

interactive model:


Zinc binding site 3 out of 5 in 3ivb


Zinc binding site 3 out of 5 in 3ivb
Click to enlarge		stereopicture of Zinc binding site 3 out of 5 in 3ivb
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3ivb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Glu97, A: Arg99, A: Arg124, A: Hoh12, A: Hoh241,

conact list:


AtomAtomDistance (A)
ZnO A:Glu974.40
ZnOE1 A:Glu972.07
ZnCB A:Glu973.32
ZnOE2 A:Glu974.20
ZnCD A:Glu973.07
ZnC A:Glu974.45
ZnCG A:Glu973.42
ZnCA A:Glu974.51
ZnNE A:Arg994.49
ZnNH2 A:Arg994.81
ZnCZ A:Arg1244.77
ZnNH2 A:Arg1244.58
ZnNH1 A:Arg1244.09
ZnO A:Hoh122.29
ZnO A:Hoh2413.51

interactive model:


Zinc binding site 4 out of 5 in 3ivb


Zinc binding site 4 out of 5 in 3ivb
Click to enlarge		stereopicture of Zinc binding site 4 out of 5 in 3ivb
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3ivb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Cys44, A: Arg45, A: Glu46, A: Glu47, A: Zn1, A: Zn5, A: Hoh8, A: Hoh217, A: Hoh218, A: Hoh224, A: Hoh226, A: Hoh240,

conact list:


AtomAtomDistance (A)
ZnN A:Cys444.98
ZnCB A:Cys443.27
ZnSG A:Cys442.32
ZnC A:Cys444.67
ZnCA A:Cys443.84
ZnN A:Arg454.81
ZnOE2 A:Glu464.07
ZnOE2 A:Glu474.86
ZnZN A:Zn13.32
ZnZN A:Zn53.77
ZnO A:Hoh82.84
ZnO A:Hoh2173.70
ZnO A:Hoh2182.65
ZnO A:Hoh2243.96
ZnO A:Hoh2264.90
ZnO A:Hoh2402.45

interactive model:


Zinc binding site 5 out of 5 in 3ivb


Zinc binding site 5 out of 5 in 3ivb
Click to enlarge		stereopicture of Zinc binding site 5 out of 5 in 3ivb
Click to enlarge		Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3ivb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Cys44, A: Arg45, A: Glu46, A: Zn4, A: Hoh8, A: Hoh217, A: Hoh218, A: Hoh224, A: Hoh225,

conact list:


AtomAtomDistance (A)
ZnSG A:Cys444.63
ZnCZ A:Arg454.94
ZnNE A:Arg454.73
ZnNH2 A:Arg454.38
ZnN A:Glu465.00
ZnOE1 A:Glu463.14
ZnCB A:Glu464.89
ZnOE2 A:Glu462.27
ZnCD A:Glu462.94
ZnCG A:Glu464.22
ZnZN A:Zn43.77
ZnO A:Hoh84.41
ZnO A:Hoh2174.57
ZnO A:Hoh2182.28
ZnO A:Hoh2243.16
ZnO A:Hoh2252.39

interactive model:
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