Sodium in PDB 6m6j: uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats

The binding sites of Sodium atom in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats (pdb code 6m6j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats, PDB code: 6m6j:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:0.0 occ:1.00 OP2 A:DG4 2.2 0.0 1.0 OP2 A:3DR5 2.2 0.0 1.0 H5' A:DG4 2.6 0.0 1.0 P A:DG4 3.5 0.0 1.0 C5' A:DG4 3.5 0.0 1.0 P A:3DR5 3.7 0.0 1.0 O5' A:DG4 3.7 0.0 1.0 O3' A:DT3 4.2 0.0 1.0 H5'' A:DG4 4.2 0.0 1.0 H4' A:DG4 4.4 0.0 1.0 H3' A:DG4 4.4 0.0 1.0 C4' A:DG4 4.4 0.0 1.0 O3' A:DG4 4.5 0.0 1.0 O5' A:3DR5 4.5 0.0 1.0 OP1 A:3DR5 4.6 0.0 1.0 C3' A:DG4 4.6 0.0 1.0 OP1 A:DG4 4.7 0.0 1.0

Sodium binding site 2 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.0 occ:1.00 OP2 A:DC6 2.2 0.0 1.0 O3' A:3DR5 2.5 0.0 1.0 P A:DC6 2.9 0.0 1.0 H5' A:DC6 3.5 0.0 1.0 C3' A:3DR5 3.7 0.0 1.0 H2'' A:3DR5 3.8 0.0 1.0 H3' A:3DR5 3.9 0.0 1.0 H5'' A:DC6 3.9 0.0 1.0 O5' A:DC6 4.0 0.0 1.0 C5' A:DC6 4.0 0.0 1.0 OP1 A:DC6 4.1 0.0 1.0 C2' A:3DR5 4.1 0.0 1.0 H2' A:3DR5 4.2 0.0 1.0

Sodium binding site 3 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.0 occ:1.00 OP1 A:DG4 2.2 0.0 1.0 OP2 A:DT3 2.3 0.0 1.0 H5'' A:DT3 2.6 0.0 1.0 H3' A:DT3 2.8 0.0 1.0 P A:DT3 2.9 0.0 1.0 O5' A:DT3 3.0 0.0 1.0 OP1 A:DT3 3.1 0.0 1.0 C5' A:DT3 3.3 0.0 1.0 P A:DG4 3.7 0.0 1.0 C3' A:DT3 3.7 0.0 1.0 H5' A:DT3 4.1 0.0 1.0 C4' A:DT3 4.1 0.0 1.0 O3' A:DT3 4.1 0.0 1.0 O3' A:DT2 4.4 0.0 1.0 O5' A:DG4 4.6 0.0 1.0 H4' A:DT3 4.6 0.0 1.0 OP2 A:DG4 4.7 0.0 1.0 H2' A:DT3 4.8 0.0 1.0 C2' A:DT3 4.9 0.0 1.0

Sodium binding site 4 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.0 occ:1.00 OP1 A:DG9 2.2 0.0 1.0 OP2 A:DT8 2.2 0.0 1.0 H3' A:DT8 2.6 0.0 1.0 H5'' A:DT8 2.9 0.0 1.0 P A:DT8 3.0 0.0 1.0 OP1 A:DT8 3.2 0.0 1.0 O5' A:DT8 3.5 0.0 1.0 C5' A:DT8 3.6 0.0 1.0 C3' A:DT8 3.6 0.0 1.0 P A:DG9 3.6 0.0 1.0 O3' A:DT8 4.1 0.0 1.0 C4' A:DT8 4.2 0.0 1.0 O5' A:DG9 4.4 0.0 1.0 H5' A:DT8 4.5 0.0 1.0 H4' A:DT8 4.5 0.0 1.0 O3' A:DT7 4.6 0.0 1.0 H2' A:DT8 4.6 0.0 1.0 OP2 A:DG9 4.7 0.0 1.0 C2' A:DT8 4.7 0.0 1.0

Sodium binding site 5 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:0.0 occ:1.00 OP1 A:DC6 2.2 0.0 1.0 OP1 A:3DR5 2.2 0.0 1.0 O3' A:DG4 2.6 0.0 1.0 P A:3DR5 3.0 0.0 1.0 H4'1 A:3DR5 3.2 0.0 1.0 P A:DC6 3.5 0.0 1.0 H5' A:3DR5 3.6 0.0 1.0 H2'' A:DG4 3.7 0.0 1.0 O5' A:DC6 3.8 0.0 1.0 C3' A:DG4 3.9 0.0 1.0 O5' A:3DR5 3.9 0.0 1.0 C4' A:3DR5 4.0 0.0 1.0 C5' A:3DR5 4.0 0.0 1.0 OP2 A:3DR5 4.2 0.0 1.0 C2' A:DG4 4.2 0.0 1.0 H4' A:DG4 4.5 0.0 1.0 H2' A:DG4 4.5 0.0 1.0 O3' A:3DR5 4.5 0.0 1.0 OP2 A:DC6 4.6 0.0 1.0 H3' A:DG4 4.6 0.0 1.0 C3' A:3DR5 4.6 0.0 1.0 H3' A:3DR5 4.8 0.0 1.0 C4' A:DG4 4.8 0.0 1.0

Sodium binding site 6 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:0.0 occ:1.00 O2 A:DT8 2.3 0.0 1.0 O6 A:DG9 2.3 0.0 1.0 N7 A:DG9 2.5 0.0 1.0 C6 A:DG9 2.9 0.0 1.0 C5 A:DG9 3.0 0.0 1.0 H1' A:DT8 3.2 0.0 1.0 C2 A:DT8 3.3 0.0 1.0 H42 A:DC6 3.7 0.0 1.0 C8 A:DG9 3.7 0.0 1.0 C1' A:DT8 4.0 0.0 1.0 H41 A:DC1 4.1 0.0 1.0 N1 A:DT8 4.1 0.0 1.0 N4 A:DC1 4.2 0.0 1.0 H3 A:DT8 4.2 0.0 1.0 N1 A:DG9 4.2 0.0 1.0 H8 A:DG9 4.2 0.0 1.0 H42 A:DC1 4.2 0.0 1.0 N3 A:DT8 4.3 0.0 1.0 C4 A:DG9 4.3 0.0 1.0 N4 A:DC6 4.6 0.0 1.0 O4' A:DT8 4.6 0.0 1.0 H1 A:DG9 4.7 0.0 1.0 N9 A:DG9 4.7 0.0 1.0 H41 A:DC6 4.9 0.0 1.0 C4 A:DC1 4.9 0.0 1.0 O6 A:DG4 5.0 0.0 1.0

Sodium binding site 7 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 2.3 0.0 1.0 OP2 A:DT2 2.3 0.0 1.0 P A:DT2 2.7 0.0 1.0 O3' A:DC1 3.9 0.0 1.0 O5' A:DT2 4.0 0.0 1.0 H5' A:DT2 4.0 0.0 1.0 H5'' A:DT2 4.2 0.0 1.0 C5' A:DT2 4.3 0.0 1.0 H3' A:DC1 4.5 0.0 1.0 C3' A:DC1 4.8 0.0 1.0

Sodium binding site 8 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cttg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:0.0 occ:1.00 OP1 A:DT7 2.3 0.0 1.0 OP2 A:DT7 2.3 0.0 1.0 P A:DT7 2.8 0.0 1.0 O3' A:DC6 3.9 0.0 1.0 H5' A:DT7 3.9 0.0 1.0 O5' A:DT7 4.0 0.0 1.0 H5'' A:DT7 4.0 0.0 1.0 C5' A:DT7 4.2 0.0 1.0 H3' A:DC6 4.5 0.0 1.0 C3' A:DC6 4.8 0.0 1.0

L.Wan, S.L.Lam, H.K.Lee, P.Guo. Rational Design of A Reversible MG2+/Edta-Controlled Molecular Switch Based on A Dna Minidumbbell. Chem.Commun.(Camb.) V. 56 10127 2020.
ISSN: ESSN 1364-548X
PubMed: 32870195
DOI: 10.1039/D0CC03774E