Sodium in PDB 7d0z: uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cctg Repeats at pH 5

The binding sites of Sodium atom in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cctg Repeats at pH 5 (pdb code 7d0z). 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 Cctg Repeats at pH 5, PDB code: 7d0z:
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 Cctg 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 Cctg Repeats at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:0.0 occ:1.00 OP1 A:DC6 2.4 0.0 1.0 OP1 A:DC5 2.4 0.0 1.0 O3' A:DC5 2.6 0.0 1.0 O5' A:DC5 2.6 0.0 1.0 H5 A:DC6 2.9 0.0 1.0 P A:DC5 3.0 0.0 1.0 P A:DC6 3.1 0.0 1.0 H4' A:DC5 3.2 0.0 1.0 H6 A:DC6 3.3 0.0 1.0 C3' A:DC5 3.5 0.0 1.0 O3' A:DG4 3.5 0.0 1.0 C4' A:DC5 3.7 0.0 1.0 C5' A:DC5 3.7 0.0 1.0 H3' A:DC5 3.7 0.0 1.0 C5 A:DC6 3.7 0.0 1.0 C6 A:DC6 3.9 0.0 1.0 OP2 A:DC6 4.0 0.0 1.0 H5' A:DC5 4.1 0.0 1.0 O5' A:DC6 4.3 0.0 1.0 OP2 A:DC5 4.4 0.0 1.0 H5'' A:DC5 4.5 0.0 1.0 H2'' A:DG4 4.8 0.0 1.0 H5' A:DC6 4.8 0.0 1.0 H1' A:DC5 4.8 0.0 1.0 C3' A:DG4 4.8 0.0 1.0 C2' A:DC5 5.0 0.0 1.0

Sodium binding site 2 out of 5 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cctg 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 Cctg Repeats at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.0 occ:1.00 OP2 A:DC5 2.3 0.0 1.0 OP1 A:DG4 2.4 0.0 1.0 OP2 A:DG4 2.7 0.0 1.0 H5' A:DG4 2.7 0.0 1.0 P A:DG4 2.9 0.0 1.0 H4' A:DG4 3.1 0.0 1.0 C5' A:DG4 3.4 0.0 1.0 O5' A:DG4 3.6 0.0 1.0 P A:DC5 3.7 0.0 1.0 C4' A:DG4 3.7 0.0 1.0 O3' A:DG4 4.3 0.0 1.0 H3' A:DG4 4.3 0.0 1.0 C3' A:DG4 4.3 0.0 1.0 OP1 A:DC5 4.3 0.0 1.0 H5'' A:DG4 4.4 0.0 1.0 O3' A:DT3 4.4 0.0 1.0 H4' A:DT3 4.6 0.0 1.0 H5'' A:DC5 4.8 0.0 1.0 O5' A:DC5 4.9 0.0 1.0 O4' A:DG4 4.9 0.0 1.0

Sodium binding site 3 out of 5 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cctg 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 Cctg Repeats at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.0 occ:1.00 OP1 A:DT7 2.3 0.0 1.0 OP1 A:DG8 2.3 0.0 1.0 H3' A:DT7 2.4 0.0 1.0 P A:DT7 3.4 0.0 1.0 O5' A:DT7 3.4 0.0 1.0 C3' A:DT7 3.5 0.0 1.0 P A:DG8 3.5 0.0 1.0 O5' A:DG8 3.8 0.0 1.0 O3' A:DT7 3.9 0.0 1.0 OP2 A:DT7 4.3 0.0 1.0 H2' A:DT7 4.3 0.0 1.0 C4' A:DT7 4.4 0.0 1.0 C2' A:DT7 4.4 0.0 1.0 C5' A:DT7 4.5 0.0 1.0 H4' A:DT7 4.6 0.0 1.0 H2'' A:DT7 4.6 0.0 1.0 O3' A:DC6 4.7 0.0 1.0 H5' A:DG8 4.8 0.0 1.0 OP2 A:DG8 4.8 0.0 1.0 C5' A:DG8 4.9 0.0 1.0

Sodium binding site 4 out of 5 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Cctg 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 Cctg Repeats at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.0 occ:1.00 OP2 A:DG8 2.4 0.0 1.0 O3' A:DT7 2.5 0.0 1.0 P A:DG8 3.0 0.0 1.0 H1' A:DT7 3.1 0.0 1.0 N7 A:DG8 3.3 0.0 1.0 C8 A:DG8 3.4 0.0 1.0 H8 A:DG8 3.4 0.0 1.0 H5'' A:DG8 3.5 0.0 1.0 O5' A:DG8 3.6 0.0 1.0 C3' A:DT7 3.7 0.0 1.0 H4' A:DT7 3.8 0.0 1.0 C1' A:DT7 3.9 0.0 1.0 C5 A:DG8 3.9 0.0 1.0 O4' A:DT7 4.0 0.0 1.0 C4' A:DT7 4.1 0.0 1.0 N9 A:DG8 4.1 0.0 1.0 C5' A:DG8 4.1 0.0 1.0 C2' A:DT7 4.3 0.0 1.0 OP1 A:DG8 4.3 0.0 1.0 H2'' A:DT7 4.4 0.0 1.0 C4 A:DG8 4.4 0.0 1.0 H3' A:DT7 4.5 0.0 1.0 H2' A:DG8 4.5 0.0 1.0 C6 A:DG8 4.8 0.0 1.0 O4' A:DG8 4.8 0.0 1.0 O2 A:DT7 4.9 0.0 1.0 H5' A:DG8 4.9 0.0 1.0 C1' A:DG8 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 Cctg 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 Cctg 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:DC2 2.4 0.0 1.0 OP2 A:DC2 2.4 0.0 1.0 P A:DC2 2.8 0.0 1.0 H5'' A:DC2 3.9 0.0 1.0 O5' A:DC2 4.0 0.0 1.0 O3' A:DCZ1 4.1 0.0 1.0 H3' A:DCZ1 4.1 0.0 1.0 C5' A:DC2 4.4 0.0 1.0 H5' A:DC2 4.4 0.0 1.0 C3' A:DCZ1 4.6 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