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Zinc in the structure of Structural Basis For Translation Termination on The 70S Ribosome. This File Contains The 30S Subunit, Release Factor 1 (RF1), Two Trna, and Mrna Molecules of The Second 70S Ribosome. the Entire Crystal Structure Contains Two 70S Ribosomes As Described in Remark 400. (pdb 3d5c)

The binding sites of Zinc atom in the structure of Structural Basis For Translation Termination on The 70S Ribosome. This File Contains The 30S Subunit, Release Factor 1 (RF1), Two Trna, and Mrna Molecules of The Second 70S Ribosome. the Entire Crystal Structure Contains Two 70S Ribosomes As Described in Remark 400. (pdb code 3d5c). This binding sites where shown with 5.0 Angstroms radius around Zinc atom.
The 3d5c structure was solved by M.LAURBERG, H.ASAHARA, A.KOROSTELEV, J.ZHU, S.TRAKHANOV, H.F.NOLLER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)49.9-3.2
Space groupP212121
a (A)210.130
b (A)454.390
c (A)616.450
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)29.2
Rfree (%)31.9

Zinc Binding Sites:

Zinc binding site 1 out of 2 in 3d5c


Zinc binding site 1 out of 2 in 3d5c
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stereopicture of Zinc binding site 1 out of 2 in 3d5c
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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3d5c. 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: D: Cys9, D: Cys12, D: Leu19, D: Leu21, D: Cys26, D: Lys30, D: Cys31, D: Ala32,

conact list:


AtomAtomDistance (A)
ZnO D:Cys94.89
ZnCB D:Cys93.71
ZnSG D:Cys92.48
ZnCA D:Cys94.15
ZnCB D:Cys124.54
ZnSG D:Cys123.52
ZnO D:Leu193.98
ZnCD1 D:Leu213.73
ZnCG D:Leu214.71
ZnCB D:Cys264.08
ZnSG D:Cys262.67
ZnCA D:Cys264.49
ZnO D:Lys304.39
ZnC D:Lys304.84
ZnO D:Cys312.29
ZnN D:Cys314.38
ZnCB D:Cys313.55
ZnSG D:Cys312.95
ZnC D:Cys312.80
ZnCA D:Cys313.04
ZnN D:Ala323.89
ZnCB D:Ala324.12
ZnCA D:Ala324.59

interactive model:


Zinc binding site 2 out of 2 in 3d5c


Zinc binding site 2 out of 2 in 3d5c
Click to enlarge
stereopicture of Zinc binding site 2 out of 2 in 3d5c
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3d5c. 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: N: Cys24, N: Arg26, N: Cys27, N: Gly28, N: Arg29, N: Cys40, N: Cys43,

conact list:


AtomAtomDistance (A)
ZnCB N:Cys244.17
ZnSG N:Cys242.99
ZnN N:Arg264.71
ZnCB N:Arg263.78
ZnC N:Arg264.15
ZnCA N:Arg264.42
ZnO N:Cys274.18
ZnN N:Cys273.13
ZnCB N:Cys273.58
ZnSG N:Cys272.44
ZnC N:Cys273.60
ZnCA N:Cys273.57
ZnN N:Gly283.66
ZnC N:Gly284.58
ZnCA N:Gly284.52
ZnN N:Arg294.21
ZnCB N:Arg294.38
ZnCA N:Arg294.95
ZnN N:Cys404.22
ZnCB N:Cys403.55
ZnSG N:Cys402.81
ZnCA N:Cys404.49
ZnN N:Cys434.45
ZnCB N:Cys433.50
ZnSG N:Cys433.11
ZnCA N:Cys434.61

interactive model:




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