Sodium in PDB 6j37: Dna Minidumbbell Structure of Two Cttg Repeats

The binding sites of Sodium atom in the Dna Minidumbbell Structure of Two Cttg Repeats (pdb code 6j37). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Dna Minidumbbell Structure of Two Cttg Repeats, PDB code: 6j37:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Dna Minidumbbell Structure of Two Cttg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Minidumbbell Structure of Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:0.0 occ:1.00 H4' A:DC5 2.4 0.0 1.0 OP1 A:DC5 2.6 0.0 1.0 O3' A:DC5 2.9 0.0 1.0 H5' A:DC5 3.0 0.0 1.0 C4' A:DC5 3.1 0.0 1.0 C3' A:DC5 3.3 0.0 1.0 H3' A:DC5 3.4 0.0 1.0 C5' A:DC5 3.5 0.0 1.0 O3' A:DG4 3.6 0.0 1.0 P A:DC5 3.6 0.0 1.0 P A:DT6 3.9 0.0 1.0 O5' A:DC5 4.0 0.0 1.0 OP1 A:DT6 4.0 0.0 1.0 OP2 A:DT6 4.3 0.0 1.0 O4' A:DC5 4.3 0.0 1.0 H72 A:DT6 4.4 0.0 1.0 H5'' A:DC5 4.4 0.0 1.0 H4' A:DG4 4.4 0.0 1.0 C2' A:DC5 4.8 0.0 1.0 C3' A:DG4 4.9 0.0 1.0 OP2 A:DC5 5.0 0.0 1.0

Sodium binding site 2 out of 7 in the Dna Minidumbbell Structure of Two Cttg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Minidumbbell Structure of Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.0 occ:1.00 H5'' A:DT7 2.4 0.0 1.0 OP1 A:DG8 2.5 0.0 1.0 O5' A:DT7 2.7 0.0 1.0 O5' A:DG8 2.8 0.0 1.0 C5' A:DT7 3.0 0.0 1.0 P A:DG8 3.2 0.0 1.0 H5' A:DT7 3.9 0.0 1.0 C4' A:DT7 3.9 0.0 1.0 H4' A:DT7 3.9 0.0 1.0 H3' A:DT7 4.0 0.0 1.0 C5' A:DG8 4.1 0.0 1.0 H4' A:DG8 4.1 0.0 1.0 P A:DT7 4.1 0.0 1.0 O4' A:DG8 4.1 0.0 1.0 O3' A:DT7 4.2 0.0 1.0 C3' A:DT7 4.2 0.0 1.0 OP1 A:DT7 4.3 0.0 1.0 C4' A:DG8 4.3 0.0 1.0 NA A:NA105 4.4 0.0 1.0 OP2 A:DG8 4.4 0.0 1.0 H5'' A:DG8 4.6 0.0 1.0 H5' A:DG8 4.7 0.0 1.0 O3' A:DT6 4.8 0.0 1.0 H1' A:DT6 4.9 0.0 1.0

Sodium binding site 3 out of 7 in the Dna Minidumbbell Structure of Two Cttg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Minidumbbell Structure of Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.0 occ:1.00 H5'' A:DT3 2.3 0.0 1.0 OP1 A:DG4 2.5 0.0 1.0 H3' A:DT3 2.8 0.0 1.0 C5' A:DT3 3.3 0.0 1.0 C3' A:DT3 3.6 0.0 1.0 P A:DG4 3.7 0.0 1.0 C4' A:DT3 3.8 0.0 1.0 O5' A:DT3 3.9 0.0 1.0 OP1 A:DT3 3.9 0.0 1.0 H4' A:DT3 4.0 0.0 1.0 H5' A:DT3 4.1 0.0 1.0 O3' A:DT3 4.1 0.0 1.0 OP2 A:DG4 4.3 0.0 1.0 P A:DT3 4.4 0.0 1.0 OP2 A:DT3 4.7 0.0 1.0 H2' A:DT3 4.8 0.0 1.0 C2' A:DT3 4.9 0.0 1.0 H1' A:DT2 4.9 0.0 1.0 H5' A:DG4 5.0 0.0 1.0

Sodium binding site 4 out of 7 in the Dna Minidumbbell Structure of Two Cttg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Dna Minidumbbell Structure of Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.0 occ:1.00 OP2 A:DC5 2.5 0.0 1.0 H3' A:DG4 2.5 0.0 1.0 H2' A:DG4 3.3 0.0 1.0 C3' A:DG4 3.4 0.0 1.0 C2' A:DG4 3.7 0.0 1.0 P A:DC5 3.7 0.0 1.0 O3' A:DG4 3.9 0.0 1.0 H2'' A:DG4 3.9 0.0 1.0 O5' A:DG4 4.3 0.0 1.0 OP2 A:DG4 4.3 0.0 1.0 C4' A:DG4 4.7 0.0 1.0 O5' A:DC5 4.7 0.0 1.0 H5'' A:DG4 4.8 0.0 1.0 OP1 A:DC5 4.8 0.0 1.0 C5' A:DG4 4.8 0.0 1.0 P A:DG4 5.0 0.0 1.0

Sodium binding site 5 out of 7 in the Dna Minidumbbell Structure of Two Cttg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Dna Minidumbbell Structure of Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:0.0 occ:1.00 OP1 A:DT7 2.5 0.0 1.0 OP1 A:DG8 2.5 0.0 1.0 H3' A:DT7 2.6 0.0 1.0 P A:DT7 3.5 0.0 1.0 C3' A:DT7 3.6 0.0 1.0 P A:DG8 3.6 0.0 1.0 O5' A:DT7 3.6 0.0 1.0 O3' A:DT7 3.8 0.0 1.0 OP2 A:DT7 4.0 0.0 1.0 H2' A:DT7 4.2 0.0 1.0 OP2 A:DG8 4.3 0.0 1.0 NA A:NA102 4.4 0.0 1.0 C2' A:DT7 4.5 0.0 1.0 C4' A:DT7 4.7 0.0 1.0 C5' A:DT7 4.7 0.0 1.0 O3' A:DT6 4.9 0.0 1.0 H2'' A:DT7 4.9 0.0 1.0 O5' A:DG8 4.9 0.0 1.0

Sodium binding site 6 out of 7 in the Dna Minidumbbell Structure of Two Cttg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Dna Minidumbbell Structure of Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:0.0 occ:1.00 O6 A:DG8 2.6 0.0 1.0 O2 A:DT7 2.6 0.0 1.0 N7 A:DG8 2.8 0.0 1.0 H1' A:DT7 2.9 0.0 1.0 C6 A:DG8 3.2 0.0 1.0 C5 A:DG8 3.3 0.0 1.0 C2 A:DT7 3.6 0.0 1.0 C1' A:DT7 3.9 0.0 1.0 C8 A:DG8 4.0 0.0 1.0 H42 A:DC1 4.1 0.0 1.0 N1 A:DT7 4.2 0.0 1.0 H42 A:DC5 4.2 0.0 1.0 N4 A:DC1 4.3 0.0 1.0 H41 A:DC1 4.4 0.0 1.0 H2'' A:DT7 4.4 0.0 1.0 H8 A:DG8 4.5 0.0 1.0 N1 A:DG8 4.5 0.0 1.0 C4 A:DG8 4.6 0.0 1.0 N3 A:DT7 4.7 0.0 1.0 O4' A:DT7 4.8 0.0 1.0 C2' A:DT7 4.8 0.0 1.0 H3 A:DT7 4.8 0.0 1.0 H1 A:DG8 4.9 0.0 1.0 N4 A:DC5 5.0 0.0 1.0 N9 A:DG8 5.0 0.0 1.0

Sodium binding site 7 out of 7 in the Dna Minidumbbell Structure of Two Cttg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Dna Minidumbbell Structure of Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:0.0 occ:1.00 OP1 A:DT2 2.6 0.0 1.0 OP2 A:DT2 2.6 0.0 1.0 P A:DT2 3.0 0.0 1.0 O3' A:DC1 4.2 0.0 1.0 O5' A:DT2 4.2 0.0 1.0 HO5' A:DC1 4.3 0.0 1.0 H5' A:DT2 4.5 0.0 1.0 O5' A:DC1 4.6 0.0 1.0 H4' A:DC1 4.7 0.0 1.0 C5' A:DT2 4.9 0.0 1.0

P.Guo, S.L.Lam. Unprecedented Hydrophobic Stabilizations From A Reverse Wobble T·T Mispair in Dna Minidumbbell. J.Biomol.Struct.Dyn. 1 2019.
ISSN: ESSN 1538-0254
PubMed: 31107180
DOI: 10.1080/07391102.2019.1621211