Sodium in PDB 7d0y: uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5

The binding sites of Sodium atom in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5 (pdb code 7d0y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5, PDB code: 7d0y:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5


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 Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:0.0 occ:1.00 OP2 A:DC5 2.2 0.0 1.0 OP2 A:DG4 2.2 0.0 1.0 H5' A:DG4 2.3 0.0 1.0 O5' A:DG4 3.0 0.0 1.0 C5' A:DG4 3.0 0.0 1.0 P A:DG4 3.2 0.0 1.0 H4' A:DG4 3.6 0.0 1.0 P A:DC5 3.7 0.0 1.0 C4' A:DG4 3.8 0.0 1.0 H5'' A:DG4 3.9 0.0 1.0 OP1 A:DG4 4.2 0.0 1.0 H3' A:DG4 4.2 0.0 1.0 O5' A:DC5 4.3 0.0 1.0 C3' A:DG4 4.3 0.0 1.0 O3' A:DG4 4.4 0.0 1.0 O3' A:DT3 4.4 0.0 1.0 OP1 A:DC5 4.8 0.0 1.0

Sodium binding site 2 out of 5 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5


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 Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.0 occ:1.00 OP1 A:DG8 2.2 0.0 1.0 OP1 A:DT7 2.2 0.0 1.0 H3' A:DT7 2.7 0.0 1.0 H5'' A:DT7 3.0 0.0 1.0 P A:DG8 3.6 0.0 1.0 P A:DT7 3.6 0.0 1.0 C3' A:DT7 3.7 0.0 1.0 C5' A:DT7 3.9 0.0 1.0 O3' A:DT7 4.0 0.0 1.0 O5' A:DT7 4.1 0.0 1.0 C4' A:DT7 4.3 0.0 1.0 O3' A:5CM6 4.4 0.0 1.0 O5' A:DG8 4.5 0.0 1.0 OP2 A:DG8 4.6 0.0 1.0 H4' A:DT7 4.6 0.0 1.0 OP2 A:DT7 4.7 0.0 1.0 H2' A:DT7 4.7 0.0 1.0 H5' A:DT7 4.8 0.0 1.0 C2' A:DT7 4.8 0.0 1.0

Sodium binding site 3 out of 5 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5


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 Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.0 occ:1.00 OP2 A:DT3 2.2 0.0 1.0 OP2 A:5CM2 2.2 0.0 1.0 H3' A:5CM2 2.4 0.0 1.0 C3' A:5CM2 3.4 0.0 1.0 H2'2 A:DCZ1 3.4 0.0 1.0 H72 A:DT3 3.5 0.0 1.0 P A:DT3 3.6 0.0 1.0 P A:5CM2 3.7 0.0 1.0 H5'' A:5CM2 3.8 0.0 1.0 O3' A:5CM2 3.8 0.0 1.0 H2' A:5CM2 4.1 0.0 1.0 C2' A:5CM2 4.1 0.0 1.0 H71 A:DT3 4.2 0.0 1.0 H2'' A:5CM2 4.2 0.0 1.0 O5' A:DT3 4.3 0.0 1.0 C7 A:DT3 4.3 0.0 1.0 C5' A:5CM2 4.4 0.0 1.0 O5' A:5CM2 4.4 0.0 1.0 C4' A:5CM2 4.4 0.0 1.0 C2' A:DCZ1 4.5 0.0 1.0 O3' A:DCZ1 4.6 0.0 1.0 OP1 A:5CM2 4.6 0.0 1.0 H6 A:DT3 4.7 0.0 1.0 OP1 A:DT3 4.7 0.0 1.0 H73 A:DT3 4.9 0.0 1.0 H2'1 A:DCZ1 4.9 0.0 1.0 H4' A:5CM2 4.9 0.0 1.0 C3' A:DCZ1 5.0 0.0 1.0

Sodium binding site 4 out of 5 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5


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 Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.0 occ:1.00 OP1 A:DC5 2.2 0.0 1.0 OP1 A:5CM6 2.3 0.0 1.0 O3' A:DC5 2.4 0.0 1.0 H5A3 A:5CM6 2.9 0.0 1.0 P A:5CM6 3.0 0.0 1.0 H4' A:DC5 3.0 0.0 1.0 H5' A:DC5 3.2 0.0 1.0 P A:DC5 3.4 0.0 1.0 H5A2 A:5CM6 3.4 0.0 1.0 C3' A:DC5 3.5 0.0 1.0 O3' A:DG4 3.6 0.0 1.0 C4' A:DC5 3.6 0.0 1.0 C5A A:5CM6 3.7 0.0 1.0 C5' A:DC5 3.7 0.0 1.0 H3' A:DC5 3.9 0.0 1.0 H6 A:5CM6 3.9 0.0 1.0 O5' A:DC5 4.0 0.0 1.0 O5' A:5CM6 4.1 0.0 1.0 OP2 A:5CM6 4.1 0.0 1.0 H5A1 A:5CM6 4.5 0.0 1.0 C5 A:5CM6 4.5 0.0 1.0 C6 A:5CM6 4.5 0.0 1.0 H2'' A:DG4 4.6 0.0 1.0 H5'' A:DC5 4.7 0.0 1.0 OP2 A:DC5 4.7 0.0 1.0 H1' A:DC5 4.8 0.0 1.0 C2' A:DC5 4.9 0.0 1.0 C3' A:DG4 4.9 0.0 1.0 O4' A:DC5 4.9 0.0 1.0 H5' A:5CM6 4.9 0.0 1.0

Sodium binding site 5 out of 5 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5


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 Structures of the Dna Minidumbbell Formed By Two Cmctg Repeats at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:0.0 occ:1.00 OP1 A:DG4 2.2 0.0 1.0 OP1 A:DT3 2.2 0.0 1.0 H3' A:DT3 2.7 0.0 1.0 H5'' A:DT3 3.2 0.0 1.0 P A:DT3 3.6 0.0 1.0 P A:DG4 3.6 0.0 1.0 C3' A:DT3 3.6 0.0 1.0 C5' A:DT3 4.0 0.0 1.0 O3' A:DT3 4.0 0.0 1.0 O3' A:5CM2 4.1 0.0 1.0 O5' A:DT3 4.1 0.0 1.0 O5' A:DG4 4.3 0.0 1.0 C4' A:DT3 4.3 0.0 1.0 H4' A:DT3 4.5 0.0 1.0 H2' A:DT3 4.7 0.0 1.0 OP2 A:DG4 4.7 0.0 1.0 C2' A:DT3 4.8 0.0 1.0 OP2 A:DT3 4.8 0.0 1.0 H5' A:DT3 4.9 0.0 1.0

L.Wan, J.Yi, S.L.Lam, H.K.Lee, P.Guo. 5-Methylcytosine Substantially Enhances the Thermal Stability of Dna Minidumbbell Chemistry 2021.
ISSN: ISSN 0947-6539
DOI: 10.1002/CHEM.202005410