Sodium in PDB 1s47: Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2

The structure of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2, PDB code: 1s47 was solved by C.Caceres, G.Wright, C.Gouyette, G.Parkinson, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.84 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.319, 56.341, 51.746, 90.00, 99.17, 90.00
R / Rfree (%)	22.4 / 31.1

The structure of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2 also contains other interesting chemical elements:

Thallium

(Tl)

6 atoms

The binding sites of Sodium atom in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2 (pdb code 1s47). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2, PDB code: 1s47:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1514 b:4.4 occ:1.00 O6 C:DG322 2.8 4.8 1.0 O6 B:DG212 2.8 21.4 1.0 O4 A:DT101 2.9 30.5 1.0 O6 D:DG432 2.9 18.3 1.0 O6 A:DG102 2.9 21.3 1.0 O4 C:DT321 2.9 14.2 1.0 TL D:TL1704 3.4 28.8 0.4 C6 D:DG432 3.7 18.2 1.0 C6 C:DG322 3.8 6.6 1.0 C6 B:DG212 3.8 22.4 1.0 C6 A:DG102 3.8 19.6 1.0 C4 A:DT101 3.8 28.4 1.0 C4 C:DT321 3.9 12.8 1.0 N1 D:DG432 3.9 16.6 1.0 O4 B:DT211 4.0 41.8 1.0 O4 D:DT431 4.1 16.5 1.0 N1 A:DG102 4.1 18.1 1.0 N1 B:DG212 4.2 21.9 1.0 N1 C:DG322 4.3 6.8 1.0 N3 B:DT211 4.4 41.0 1.0 N3 A:DT101 4.4 27.5 1.0 N3 C:DT321 4.6 11.4 1.0 N3 D:DT431 4.6 17.9 1.0 C4 B:DT211 4.7 41.2 1.0 C4 D:DT431 4.8 17.2 1.0 C5 C:DT321 4.9 12.2 1.0 C5 A:DT101 4.9 29.0 1.0 C5 C:DG322 4.9 8.6 1.0 C5 B:DG212 5.0 23.1 1.0

Sodium binding site 2 out of 7 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1515 b:24.2 occ:1.00 O6 D:DG435 2.7 18.7 1.0 O6 A:DG105 2.7 31.5 1.0 O6 B:DG215 2.7 6.9 1.0 O6 C:DG325 2.7 14.3 1.0 O6 D:DG434 3.2 12.4 1.0 N1 A:DG105 3.4 32.3 1.0 TL B:TL1703 3.5 47.7 0.6 C6 A:DG105 3.5 32.0 1.0 O6 A:DG104 3.5 3.2 1.0 O6 C:DG324 3.6 21.0 1.0 O6 B:DG214 3.6 15.5 1.0 C6 B:DG215 3.6 6.5 1.0 C6 D:DG435 3.7 19.2 1.0 N1 B:DG215 3.7 4.1 1.0 C6 C:DG325 3.8 17.7 1.0 N1 B:DG214 3.8 16.8 1.0 N1 A:DG104 3.8 4.1 1.0 C6 D:DG434 3.8 12.9 1.0 N1 D:DG435 3.9 18.0 1.0 C6 A:DG104 3.9 7.5 1.0 C6 B:DG214 4.0 18.1 1.0 N1 D:DG434 4.0 11.2 1.0 N1 C:DG325 4.1 17.8 1.0 C6 C:DG324 4.4 20.8 1.0 C2 A:DG105 4.7 32.8 1.0 N1 C:DG324 4.8 21.8 1.0 C2 B:DG214 4.8 15.5 1.0 C2 A:DG104 4.8 6.5 1.0 C5 A:DG105 4.9 31.7 1.0 C5 D:DG434 4.9 13.9 1.0 C5 B:DG215 4.9 8.1 1.0

Sodium binding site 3 out of 7 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na1505 b:3.2 occ:1.00 O6 I:DG1022 2.7 8.7 1.0 O6 J:DG1132 2.7 14.6 1.0 O6 H:DG912 2.8 7.2 1.0 O6 K:DG1242 2.8 10.5 1.0 O6 L:DG1352 3.0 9.2 1.0 O6 G:DG802 3.0 21.8 1.0 O6 E:DG582 3.1 23.2 1.0 O6 F:DG692 3.1 13.0 1.0 NA H:NA1506 3.3 3.2 1.0 TL I:TL1700 3.4 55.6 0.6 C6 H:DG912 3.6 8.2 1.0 C6 I:DG1022 3.7 9.5 1.0 C6 J:DG1132 3.8 16.7 1.0 C6 E:DG582 3.8 23.2 1.0 C6 F:DG692 3.8 13.5 1.0 N1 H:DG912 3.9 5.5 1.0 N1 F:DG692 3.9 14.3 1.0 C6 G:DG802 3.9 22.4 1.0 C6 L:DG1352 3.9 10.1 1.0 C6 K:DG1242 3.9 10.4 1.0 N1 I:DG1022 3.9 8.1 1.0 N1 E:DG582 4.0 23.6 1.0 N1 L:DG1352 4.1 9.3 1.0 N1 J:DG1132 4.2 17.9 1.0 N1 G:DG802 4.2 22.6 1.0 N1 K:DG1242 4.2 10.4 1.0 C5 H:DG912 4.8 8.6 1.0 C5 I:DG1022 5.0 8.1 1.0

Sodium binding site 4 out of 7 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na1507 b:11.4 occ:1.00 O6 H:DG915 2.7 26.0 1.0 O6 H:DG914 2.8 17.1 1.0 O6 E:DG585 2.8 9.6 1.0 O6 F:DG695 2.9 8.2 1.0 O6 E:DG584 3.0 18.7 1.0 O6 G:DG805 3.1 18.8 1.0 O6 G:DG804 3.2 9.3 1.0 NA F:NA1510 3.3 3.2 1.0 O6 F:DG694 3.4 22.4 1.0 C6 H:DG914 3.6 15.7 1.0 C6 E:DG584 3.6 16.9 1.0 C6 F:DG695 3.7 11.1 1.0 C6 H:DG915 3.7 26.1 1.0 C6 E:DG585 3.7 8.2 1.0 N1 E:DG584 3.7 15.8 1.0 TL E:TL1701 3.7 57.2 0.7 N1 H:DG914 3.7 15.3 1.0 N1 F:DG695 3.8 12.9 1.0 N1 E:DG585 3.8 4.3 1.0 C6 G:DG805 3.9 19.3 1.0 N1 H:DG915 3.9 25.2 1.0 N1 G:DG805 3.9 20.0 1.0 C6 G:DG804 4.0 12.4 1.0 C6 F:DG694 4.2 19.9 1.0 N1 G:DG804 4.4 10.5 1.0 N1 F:DG694 4.4 15.8 1.0 C5 H:DG914 4.8 14.5 1.0 C5 E:DG584 4.9 16.6 1.0 C2 E:DG584 4.9 13.6 1.0 C5 F:DG695 5.0 10.1 1.0 C2 H:DG914 5.0 16.4 1.0 C2 F:DG695 5.0 12.8 1.0 C5 H:DG915 5.0 25.2 1.0

Sodium binding site 5 out of 7 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na1510 b:3.2 occ:1.00 O H:HOH1944 2.8 23.0 1.0 O6 F:DG695 3.0 8.2 1.0 O6 E:DG585 3.1 9.6 1.0 O6 G:DG805 3.2 18.8 1.0 O6 H:DG915 3.2 26.0 1.0 NA E:NA1507 3.3 11.4 1.0 O4 F:DT696 3.4 15.8 1.0 C6 F:DG695 3.7 11.1 1.0 C6 H:DG915 3.8 26.1 1.0 C6 E:DG585 3.8 8.2 1.0 C6 G:DG805 3.9 19.3 1.0 N1 F:DG695 3.9 12.9 1.0 N1 G:DG805 3.9 20.0 1.0 N1 H:DG915 4.0 25.2 1.0 N1 E:DG585 4.1 4.3 1.0 C4 F:DT696 4.2 19.4 1.0 N3 F:DT696 4.3 18.4 1.0 C5 H:DG915 4.9 25.2 1.0 C5 F:DG695 5.0 10.1 1.0

Sodium binding site 6 out of 7 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1506 b:3.2 occ:1.00 O6 G:DG802 2.7 21.8 1.0 O6 H:DG912 2.7 7.2 1.0 O6 F:DG693 2.8 18.7 1.0 O6 H:DG913 2.8 15.7 1.0 O6 G:DG803 2.8 22.6 1.0 O6 E:DG583 2.8 18.1 1.0 O6 E:DG582 3.0 23.2 1.0 O6 F:DG692 3.1 13.0 1.0 NA E:NA1505 3.3 3.2 1.0 TL E:TL1701 3.4 57.2 0.7 C6 H:DG912 3.5 8.2 1.0 C6 G:DG802 3.6 22.4 1.0 C6 F:DG693 3.6 19.1 1.0 N1 H:DG912 3.7 5.5 1.0 C6 E:DG583 3.7 18.9 1.0 C6 G:DG803 3.8 22.7 1.0 C6 H:DG913 3.8 12.4 1.0 C6 E:DG582 3.9 23.2 1.0 N1 F:DG693 3.9 18.2 1.0 C6 F:DG692 3.9 13.5 1.0 N1 G:DG802 4.0 22.6 1.0 N1 G:DG803 4.0 22.8 1.0 N1 E:DG583 4.0 19.5 1.0 N1 E:DG582 4.1 23.6 1.0 N1 F:DG692 4.1 14.3 1.0 N1 H:DG913 4.2 10.8 1.0 C5 H:DG912 4.7 8.6 1.0 C5 G:DG802 4.8 22.7 1.0 C5 F:DG693 4.9 18.1 1.0 C2 H:DG912 4.9 6.9 1.0 C5 E:DG583 5.0 18.7 1.0

Sodium binding site 7 out of 7 in the Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure Analysis of the Dna Quadruplex D(Tggggt)S2 within 5.0Å range: probe atom residue distance (Å) B Occ K:Na1512 b:4.6 occ:1.00 O6 K:DG1245 2.9 18.0 1.0 O6 I:DG1025 3.0 23.5 1.0 O6 L:DG1355 3.0 7.7 1.0 O6 J:DG1135 3.2 12.1 1.0 TL I:TL1705 3.4 25.1 0.4 C6 K:DG1245 3.4 18.1 1.0 N1 K:DG1245 3.4 17.0 1.0 C6 L:DG1355 3.7 10.1 1.0 C6 I:DG1025 3.9 24.5 1.0 N1 L:DG1355 3.9 8.8 1.0 C6 J:DG1135 4.0 12.2 1.0 N1 J:DG1135 4.0 12.6 1.0 N1 I:DG1025 4.1 24.4 1.0 C2 K:DG1245 4.5 18.9 1.0 C5 K:DG1245 4.6 18.9 1.0 C5 L:DG1355 4.8 9.5 1.0 N2 K:DG1245 5.0 19.6 1.0

C.Caceres, G.Wright, C.Gouyette, G.Parkinson, J.A.Subirana. A Thymine Tetrad in D(Tggggt) Quadruplexes Stabilized with Tl+1/Na+1 Ions Nucleic Acids Res. V. 32 1097 2004.
ISSN: ISSN 0305-1048
PubMed: 14960719
DOI: 10.1093/NAR/GKH269