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Sodium in PDB 3tvb: A Highly Symmetric Dna G-4 Quadruplex/Drug Complex

Protein crystallography data

The structure of A Highly Symmetric Dna G-4 Quadruplex/Drug Complex, PDB code: 3tvb was solved by G.R.Clark, P.D.Pytel, C.J.Squire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.08
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 40.209, 40.209, 49.831, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.2

Other elements in 3tvb:

The structure of A Highly Symmetric Dna G-4 Quadruplex/Drug Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the A Highly Symmetric Dna G-4 Quadruplex/Drug Complex (pdb code 3tvb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the A Highly Symmetric Dna G-4 Quadruplex/Drug Complex, PDB code: 3tvb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3tvb

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Sodium binding site 1 out of 8 in the A Highly Symmetric Dna G-4 Quadruplex/Drug Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Highly Symmetric Dna G-4 Quadruplex/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na13

b:6.0
occ:0.25
O6 A:DG1 2.8 7.3 1.0
O6 A:DG2 2.9 7.2 1.0
NA A:NA14 3.5 6.0 0.2
C6 A:DG2 3.7 7.5 1.0
C6 A:DG1 3.7 7.1 1.0
O A:HOH101 3.8 11.5 0.2
N1 A:DG1 3.9 7.3 1.0
N1 A:DG2 4.0 7.3 1.0
C5 A:DG1 4.9 7.3 1.0
C5 A:DG2 5.0 7.4 1.0

Sodium binding site 2 out of 8 in 3tvb

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Sodium binding site 2 out of 8 in the A Highly Symmetric Dna G-4 Quadruplex/Drug Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Highly Symmetric Dna G-4 Quadruplex/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na14

b:6.0
occ:0.25
O6 A:DG3 2.6 7.6 1.0
O6 A:DG2 2.8 7.2 1.0
NA A:NA13 3.5 6.0 0.2
C6 A:DG3 3.6 7.8 1.0
NA A:NA15 3.6 8.0 0.2
C6 A:DG2 3.7 7.5 1.0
N1 A:DG3 3.9 7.6 1.0
N1 A:DG2 4.0 7.3 1.0
C5 A:DG2 4.8 7.4 1.0
C5 A:DG3 4.9 8.0 1.0
O6 A:DG4 5.0 8.0 1.0

Sodium binding site 3 out of 8 in 3tvb

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Sodium binding site 3 out of 8 in the A Highly Symmetric Dna G-4 Quadruplex/Drug Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Highly Symmetric Dna G-4 Quadruplex/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na15

b:8.0
occ:0.25
O6 A:DG4 2.4 8.0 1.0
O6 A:DG3 3.2 7.6 1.0
C6 A:DG4 3.4 8.2 1.0
NA A:NA14 3.6 6.0 0.2
N1 A:DG4 3.8 8.2 1.0
C6 A:DG3 3.9 7.8 1.0
N1 A:DG3 4.2 7.6 1.0
C5 A:DG4 4.7 9.0 1.0
O A:HOH107 4.7 31.3 0.8

Sodium binding site 4 out of 8 in 3tvb

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Sodium binding site 4 out of 8 in the A Highly Symmetric Dna G-4 Quadruplex/Drug Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of A Highly Symmetric Dna G-4 Quadruplex/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na16

b:5.7
occ:0.25
O6 B:DG5 2.8 7.0 1.0
O6 B:DG6 2.9 7.2 1.0
NA B:NA17 3.5 6.0 0.2
C6 B:DG5 3.7 6.5 1.0
MG B:MG22 3.7 17.0 0.2
C6 B:DG6 3.7 6.5 1.0
N1 B:DG5 3.9 6.7 1.0
N1 B:DG6 4.0 6.7 1.0
O B:HOH102 4.2 46.1 1.0
C5 B:DG5 4.9 7.0 1.0
C5 B:DG6 5.0 6.7 1.0

Sodium binding site 5 out of 8 in 3tvb

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Sodium binding site 5 out of 8 in the A Highly Symmetric Dna G-4 Quadruplex/Drug Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of A Highly Symmetric Dna G-4 Quadruplex/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na17

b:6.0
occ:0.25
O6 B:DG7 2.6 7.9 1.0
O6 B:DG6 2.8 7.2 1.0
NA B:NA16 3.5 5.7 0.2
NA B:NA18 3.6 9.5 0.2
C6 B:DG7 3.6 7.0 1.0
C6 B:DG6 3.6 6.5 1.0
N1 B:DG7 3.9 7.3 1.0
N1 B:DG6 4.0 6.7 1.0
C5 B:DG6 4.8 6.7 1.0
C5 B:DG7 4.8 7.3 1.0

Sodium binding site 6 out of 8 in 3tvb

Go back to Sodium Binding Sites List in 3tvb
Sodium binding site 6 out of 8 in the A Highly Symmetric Dna G-4 Quadruplex/Drug Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of A Highly Symmetric Dna G-4 Quadruplex/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na18

b:9.5
occ:0.25
O6 B:DG8 2.5 8.6 1.0
O6 B:DG7 3.1 7.9 1.0
C6 B:DG8 3.4 9.1 1.0
NA B:NA17 3.6 6.0 0.2
N1 B:DG8 3.8 8.9 1.0
C6 B:DG7 3.9 7.0 1.0
NA B:NA19 4.0 55.9 0.2
N1 B:DG7 4.2 7.3 1.0
C5 B:DG8 4.8 9.3 1.0
O B:HOH110 5.0 18.6 0.2
O B:HOH109 5.0 37.3 0.8
C5 B:DG7 5.0 7.3 1.0

Sodium binding site 7 out of 8 in 3tvb

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Sodium binding site 7 out of 8 in the A Highly Symmetric Dna G-4 Quadruplex/Drug Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of A Highly Symmetric Dna G-4 Quadruplex/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na19

b:55.9
occ:0.25
O B:HOH110 2.4 18.6 0.2
O B:HOH109 2.4 37.3 0.8
MG B:MG21 3.7 48.4 0.1
O6 B:DG8 3.9 8.6 1.0
NA B:NA18 4.0 9.5 0.2
C6 B:DG8 4.3 9.1 1.0
O B:HOH111 4.4 39.0 0.2
N1 B:DG8 4.6 8.9 1.0

Sodium binding site 8 out of 8 in 3tvb

Go back to Sodium Binding Sites List in 3tvb
Sodium binding site 8 out of 8 in the A Highly Symmetric Dna G-4 Quadruplex/Drug Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of A Highly Symmetric Dna G-4 Quadruplex/Drug Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na20

b:53.9
occ:0.25
O B:HOH106 3.3 40.7 0.2
O A:HOH103 3.5 57.4 0.1
O19 B:DM111 4.9 9.9 1.0

Reference:

G.R.Clark, P.D.Pytel, C.J.Squire. The High-Resolution Crystal Structure of A Parallel Intermolecular Dna G-4 Quadruplex/Drug Complex Employing Syn Glycosyl Linkages. Nucleic Acids Res. V. 40 5731 2012.
ISSN: ISSN 0305-1048
PubMed: 22373921
DOI: 10.1093/NAR/GKS193
Page generated: Tue Dec 15 06:26:41 2020

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