Chemical elements
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Sodium in the structure of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) (pdb 1ply)






The binding sites of Sodium atom in the structure of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) (pdb code 1ply). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 1ply structure was solved by R.CHANDRASEKARAN, A.RADHA, H.-S.PARK, with Fiber diffraction technique.


Sodium Binding Sites:

Sodium binding site 1 out of 10 in 1ply


Sodium binding site 1 out of 10 in 1ply
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stereopicture of Sodium binding site 1 out of 10 in 1ply
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1ply. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres:

conact list:


AtomAtomDistance (A)

interactive model:


Sodium binding site 2 out of 10 in 1ply


Sodium binding site 2 out of 10 in 1ply
Click to enlarge
stereopicture of Sodium binding site 2 out of 10 in 1ply
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1ply. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Da1, A: Da2, A: Hoh14,

conact list:


AtomAtomDistance (A)
NaH5' A:Da13.71
NaH3' A:Da13.07
NaO3' A:Da14.25
NaC4' A:Da14.59
NaO5' A:Da14.30
NaC3' A:Da14.01
NaH4' A:Da14.74
NaC5' A:Da14.36
NaO5' A:Da24.89
NaOP1 A:Da22.79
NaP A:Da23.46
NaOP2 A:Da23.24
NaO A:Hoh142.64

interactive model:


Sodium binding site 3 out of 10 in 1ply


Sodium binding site 3 out of 10 in 1ply
Click to enlarge
stereopicture of Sodium binding site 3 out of 10 in 1ply
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1ply. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Da1, A: Na9, A: Hoh14, A: Hoh15,

conact list:


AtomAtomDistance (A)
NaH2' A:Da14.38
NaH3' A:Da14.66
NaO5' A:Da14.18
NaH8 A:Da14.21
NaOP1 A:Da12.88
NaC3' A:Da14.99
NaP A:Da14.09
NaC2' A:Da14.22
NaH2' A:Da13.29
NaNA A:Na94.28
NaO A:Hoh144.62
NaO A:Hoh152.76

interactive model:


Sodium binding site 4 out of 10 in 1ply


Sodium binding site 4 out of 10 in 1ply
Click to enlarge
stereopicture of Sodium binding site 4 out of 10 in 1ply
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1ply. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Na8, A: Hoh15,

conact list:


AtomAtomDistance (A)
NaNA A:Na84.28
NaO A:Hoh152.91

interactive model:


Sodium binding site 5 out of 10 in 1ply


Sodium binding site 5 out of 10 in 1ply
Click to enlarge
stereopicture of Sodium binding site 5 out of 10 in 1ply
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1ply. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Da2, A: Da3, A: Hoh16,

conact list:


AtomAtomDistance (A)
NaH2' A:Da23.94
NaC2' A:Da24.66
NaH2' A:Da24.49
NaH8 A:Da34.27
NaO A:Hoh163.86

interactive model:


Sodium binding site 6 out of 10 in 1ply


Sodium binding site 6 out of 10 in 1ply
Click to enlarge
stereopicture of Sodium binding site 6 out of 10 in 1ply
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1ply. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Da1, B: Dt9, B: Dt10,

conact list:


AtomAtomDistance (A)
NaH61 A:Da14.39
NaH72 B:Dt94.84
NaH72 B:Dt102.71
NaC5 B:Dt104.28
NaH71 B:Dt104.46
NaC4 B:Dt104.02
NaO4 B:Dt103.26
NaH73 B:Dt103.80
NaC7 B:Dt103.66

interactive model:


Sodium binding site 7 out of 10 in 1ply


Sodium binding site 7 out of 10 in 1ply
Click to enlarge
stereopicture of Sodium binding site 7 out of 10 in 1ply
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 1ply. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Dt9, B: Dt10, B: Hoh21,

conact list:


AtomAtomDistance (A)
NaH2' B:Dt93.25
NaH3' B:Dt94.02
NaO3' B:Dt94.70
NaC3' B:Dt94.36
NaC2' B:Dt93.93
NaH2' B:Dt93.95
NaH72 B:Dt103.86
NaC6 B:Dt104.52
NaC5 B:Dt104.59
NaH71 B:Dt102.68
NaH73 B:Dt104.30
NaP B:Dt104.46
NaC7 B:Dt103.69
NaOP2 B:Dt103.13
NaH2' B:Dt104.58
NaH6 B:Dt103.77
NaO B:Hoh213.88

interactive model:


Sodium binding site 8 out of 10 in 1ply


Sodium binding site 8 out of 10 in 1ply
Click to enlarge
stereopicture of Sodium binding site 8 out of 10 in 1ply
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 1ply. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Hoh16,

conact list:


AtomAtomDistance (A)
NaO A:Hoh163.15

interactive model:


Sodium binding site 9 out of 10 in 1ply


Sodium binding site 9 out of 10 in 1ply
Click to enlarge
stereopicture of Sodium binding site 9 out of 10 in 1ply
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 1ply. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Dt8, B: Dt9,

conact list:


AtomAtomDistance (A)
NaO3' B:Dt84.67
NaH4' B:Dt84.71
NaH5' B:Dt93.77
NaH5' B:Dt93.34
NaO5' B:Dt94.33
NaOP1 B:Dt93.16
NaP B:Dt94.26
NaC5' B:Dt93.97

interactive model:


Sodium binding site 10 out of 10 in 1ply


Sodium binding site 10 out of 10 in 1ply
Click to enlarge
stereopicture of Sodium binding site 10 out of 10 in 1ply
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 1ply. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Dt6, B: Dt7, B: Dt8, B: Hoh23,

conact list:


AtomAtomDistance (A)
NaH2' B:Dt64.92
NaH71 B:Dt74.69
NaO5' B:Dt74.82
NaP B:Dt74.48
NaOP2 B:Dt73.10
NaH2' B:Dt74.33
NaH6 B:Dt74.71
NaH71 B:Dt84.93
NaH73 B:Dt84.88
NaO B:Hoh233.19

interactive model:




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