Sodium in PDB 6iy5: uc(Nmr) Solution Structures of 5'-Attctattct-3

The binding sites of Sodium atom in the uc(Nmr) Solution Structures of 5'-Attctattct-3 (pdb code 6iy5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the uc(Nmr) Solution Structures of 5'-Attctattct-3, PDB code: 6iy5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the uc(Nmr) Solution Structures of 5'-Attctattct-3


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 5'-Attctattct-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:0.0 occ:1.00 OP1 A:DT7 2.3 0.0 1.0 O5' A:DA6 2.4 0.0 1.0 H4' A:DA6 2.6 0.0 1.0 OP1 A:DA6 2.9 0.0 1.0 P A:DA6 2.9 0.0 1.0 OP2 A:DA6 3.0 0.0 1.0 P A:DT7 3.1 0.0 1.0 O3' A:DA6 3.1 0.0 1.0 C4' A:DA6 3.3 0.0 1.0 C5' A:DA6 3.3 0.0 1.0 OP2 A:DT7 3.5 0.0 1.0 NA A:NA105 3.5 0.0 1.0 H5' A:DA6 3.7 0.0 1.0 C3' A:DA6 3.7 0.0 1.0 H3' A:DA6 4.2 0.0 1.0 H5'' A:DA6 4.3 0.0 1.0 O3' A:DT5 4.5 0.0 1.0 O4' A:DA6 4.5 0.0 1.0 O5' A:DT7 4.6 0.0 1.0 H4' A:DT5 4.7 0.0 1.0

Sodium binding site 2 out of 9 in the uc(Nmr) Solution Structures of 5'-Attctattct-3


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 5'-Attctattct-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.0 occ:1.00 O2 A:DC9 2.2 0.0 1.0 O4 A:DT10 2.4 0.0 1.0 O4 A:DT7 2.4 0.0 1.0 N6 A:DA1 2.6 0.0 1.0 H62 A:DA1 2.6 0.0 1.0 C6 A:DA1 3.0 0.0 1.0 H61 A:DA1 3.0 0.0 1.0 C2 A:DC9 3.3 0.0 1.0 N1 A:DA1 3.3 0.0 1.0 H3 A:DT7 3.4 0.0 1.0 C4 A:DT7 3.4 0.0 1.0 C4 A:DT10 3.5 0.0 1.0 H71 A:DT10 3.6 0.0 1.0 N3 A:DC9 3.8 0.0 1.0 N3 A:DT7 3.8 0.0 1.0 C5 A:DA1 3.9 0.0 1.0 H73 A:DT10 4.1 0.0 1.0 H1' A:DC9 4.2 0.0 1.0 C7 A:DT10 4.2 0.0 1.0 C5 A:DT10 4.3 0.0 1.0 C2 A:DA1 4.3 0.0 1.0 H3 A:DT10 4.4 0.0 1.0 N3 A:DT10 4.5 0.0 1.0 N1 A:DC9 4.5 0.0 1.0 N7 A:DA1 4.6 0.0 1.0 C5 A:DT7 4.7 0.0 1.0 C4 A:DA1 4.7 0.0 1.0 H73 A:DT7 4.8 0.0 1.0 C1' A:DC9 4.9 0.0 1.0 H2 A:DA1 5.0 0.0 1.0

Sodium binding site 3 out of 9 in the uc(Nmr) Solution Structures of 5'-Attctattct-3


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 5'-Attctattct-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.0 occ:1.00 O2 A:DC4 2.2 0.0 1.0 O4 A:DT5 2.3 0.0 1.0 H2' A:DC4 3.1 0.0 1.0 C2 A:DC4 3.3 0.0 1.0 C4 A:DT5 3.4 0.0 1.0 H73 A:DT5 3.8 0.0 1.0 N3 A:DC4 3.9 0.0 1.0 C2' A:DC4 3.9 0.0 1.0 H2'' A:DC4 4.0 0.0 1.0 H3 A:DT5 4.2 0.0 1.0 N3 A:DT5 4.3 0.0 1.0 H72 A:DT5 4.3 0.0 1.0 N1 A:DC4 4.3 0.0 1.0 H1' A:DC4 4.3 0.0 1.0 C5 A:DT5 4.3 0.0 1.0 C7 A:DT5 4.4 0.0 1.0 C1' A:DC4 4.4 0.0 1.0

Sodium binding site 4 out of 9 in the uc(Nmr) Solution Structures of 5'-Attctattct-3


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 5'-Attctattct-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.0 occ:1.00 OP2 A:DT10 2.2 0.0 1.0 OP1 A:DC9 2.4 0.0 1.0 OP2 A:DC9 2.4 0.0 1.0 P A:DC9 2.7 0.0 1.0 H3' A:DC9 2.8 0.0 1.0 P A:DT10 3.2 0.0 1.0 OP1 A:DT10 3.4 0.0 1.0 H5'' A:DC9 3.4 0.0 1.0 O5' A:DC9 3.5 0.0 1.0 C3' A:DC9 3.7 0.0 1.0 C5' A:DC9 3.9 0.0 1.0 O3' A:DC9 3.9 0.0 1.0 O3' A:DT8 4.2 0.0 1.0 C4' A:DC9 4.3 0.0 1.0 O5' A:DT10 4.6 0.0 1.0 H4' A:DC9 4.8 0.0 1.0 H2' A:DC9 4.8 0.0 1.0 C2' A:DC9 4.9 0.0 1.0 H5' A:DC9 4.9 0.0 1.0

Sodium binding site 5 out of 9 in the uc(Nmr) Solution Structures of 5'-Attctattct-3


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 5'-Attctattct-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:0.0 occ:1.00 OP1 A:DA6 2.2 0.0 1.0 OP1 A:DT7 2.3 0.0 1.0 H5'' A:DT5 2.6 0.0 1.0 H4' A:DA6 2.7 0.0 1.0 NA A:NA101 3.5 0.0 1.0 P A:DT7 3.6 0.0 1.0 C5' A:DT5 3.7 0.0 1.0 P A:DA6 3.7 0.0 1.0 C4' A:DA6 3.7 0.0 1.0 H1' A:DA6 3.7 0.0 1.0 O4' A:DA6 3.9 0.0 1.0 H5' A:DT5 4.0 0.0 1.0 H4' A:DT5 4.0 0.0 1.0 O5' A:DT7 4.1 0.0 1.0 O5' A:DA6 4.3 0.0 1.0 C1' A:DA6 4.3 0.0 1.0 C4' A:DT5 4.4 0.0 1.0 O3' A:DA6 4.5 0.0 1.0 OP2 A:DA6 4.5 0.0 1.0 O5' A:DT5 4.6 0.0 1.0 C3' A:DA6 4.6 0.0 1.0 C5' A:DA6 4.6 0.0 1.0 H3' A:DT5 4.6 0.0 1.0 OP2 A:DT7 4.7 0.0 1.0 OP1 A:DT5 4.7 0.0 1.0 O3' A:DT5 4.8 0.0 1.0 C3' A:DT5 4.8 0.0 1.0

Sodium binding site 6 out of 9 in the uc(Nmr) Solution Structures of 5'-Attctattct-3


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 Structures of 5'-Attctattct-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:0.0 occ:1.00 OP2 A:DT2 2.3 0.0 1.0 OP1 A:DT3 2.4 0.0 1.0 O3' A:DT2 2.5 0.0 1.0 P A:DT3 2.7 0.0 1.0 H3' A:DT2 2.9 0.0 1.0 OP2 A:DT3 3.0 0.0 1.0 C3' A:DT2 3.2 0.0 1.0 H5'' A:DT2 3.5 0.0 1.0 P A:DT2 3.6 0.0 1.0 C5' A:DT2 4.1 0.0 1.0 C4' A:DT2 4.2 0.0 1.0 O5' A:DT2 4.2 0.0 1.0 OP1 A:DT2 4.3 0.0 1.0 O5' A:DT3 4.3 0.0 1.0 C2' A:DT2 4.4 0.0 1.0 H2' A:DT2 4.5 0.0 1.0 H4' A:DT2 4.6 0.0 1.0 H2'' A:DT2 4.7 0.0 1.0 H2'' A:DA1 4.8 0.0 1.0 O3' A:DA1 4.8 0.0 1.0 H3' A:DA1 4.8 0.0 1.0

Sodium binding site 7 out of 9 in the uc(Nmr) Solution Structures of 5'-Attctattct-3


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 Structures of 5'-Attctattct-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:0.0 occ:1.00 OP1 A:DT8 2.2 0.0 1.0 O4' A:DT8 2.4 0.0 1.0 O2 A:DT8 2.5 0.0 1.0 C2 A:DT8 2.9 0.0 1.0 N1 A:DT8 2.9 0.0 1.0 C1' A:DT8 3.1 0.0 1.0 H5' A:DT8 3.5 0.0 1.0 C4' A:DT8 3.5 0.0 1.0 P A:DT8 3.6 0.0 1.0 H1' A:DT8 3.6 0.0 1.0 C5' A:DT8 3.9 0.0 1.0 N3 A:DT8 3.9 0.0 1.0 H4' A:DT8 3.9 0.0 1.0 C6 A:DT8 3.9 0.0 1.0 O5' A:DT8 4.0 0.0 1.0 H3 A:DT8 4.3 0.0 1.0 O3' A:DT7 4.3 0.0 1.0 C2' A:DT8 4.4 0.0 1.0 H6 A:DT8 4.4 0.0 1.0 H2' A:DT8 4.6 0.0 1.0 C3' A:DT8 4.7 0.0 1.0 OP2 A:DT8 4.7 0.0 1.0 C5 A:DT8 4.7 0.0 1.0 C4 A:DT8 4.8 0.0 1.0 H5'' A:DT8 4.9 0.0 1.0

Sodium binding site 8 out of 9 in the uc(Nmr) Solution Structures of 5'-Attctattct-3


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 Structures of 5'-Attctattct-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:0.0 occ:1.00 OP1 A:DT5 2.3 0.0 1.0 OP1 A:DC4 2.4 0.0 1.0 O5' A:DC4 2.4 0.0 1.0 P A:DC4 2.9 0.0 1.0 OP2 A:DT5 3.0 0.0 1.0 P A:DT5 3.0 0.0 1.0 H3' A:DC4 3.0 0.0 1.0 OP2 A:DC4 3.4 0.0 1.0 C5' A:DC4 3.6 0.0 1.0 C3' A:DC4 3.7 0.0 1.0 H5'' A:DC4 3.8 0.0 1.0 O3' A:DC4 3.9 0.0 1.0 H2'' A:DT3 3.9 0.0 1.0 C4' A:DC4 4.2 0.0 1.0 O3' A:DT3 4.3 0.0 1.0 H1' A:DT3 4.4 0.0 1.0 O5' A:DT5 4.4 0.0 1.0 H5' A:DC4 4.5 0.0 1.0 H4' A:DC4 4.6 0.0 1.0 H4' A:DT3 4.7 0.0 1.0 C2' A:DT3 4.8 0.0 1.0 H5' A:DT5 4.9 0.0 1.0

Sodium binding site 9 out of 9 in the uc(Nmr) Solution Structures of 5'-Attctattct-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of uc(Nmr) Solution Structures of 5'-Attctattct-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:0.0 occ:1.00 OP1 A:DT10 2.3 0.0 1.0 OP1 A:DT2 2.3 0.0 1.0 O5' A:DT10 2.4 0.0 1.0 O5' A:DT2 2.5 0.0 1.0 H5' A:DT2 2.8 0.0 1.0 P A:DT2 2.9 0.0 1.0 P A:DT10 2.9 0.0 1.0 C5' A:DT2 3.0 0.0 1.0 O3' A:DA1 3.3 0.0 1.0 H5'' A:DT2 3.3 0.0 1.0 H1' A:DA1 3.6 0.0 1.0 C5' A:DT10 3.7 0.0 1.0 H4' A:DT10 3.8 0.0 1.0 OP2 A:DT10 4.0 0.0 1.0 H5' A:DT10 4.0 0.0 1.0 O3' A:DC9 4.1 0.0 1.0 C4' A:DT10 4.2 0.0 1.0 OP2 A:DT2 4.3 0.0 1.0 H4' A:DC9 4.4 0.0 1.0 O4' A:DT10 4.4 0.0 1.0 C4' A:DT2 4.5 0.0 1.0 H5'' A:DT10 4.5 0.0 1.0 C3' A:DA1 4.5 0.0 1.0 C1' A:DA1 4.5 0.0 1.0 H2'' A:DA1 4.6 0.0 1.0 H4' A:DA1 4.8 0.0 1.0 C2' A:DA1 4.8 0.0 1.0 H5'' A:DC9 4.8 0.0 1.0 O4' A:DT2 4.8 0.0 1.0 O4' A:DA1 4.8 0.0 1.0

S.L.Lam, P.Guo. Minidumbbell Structures Formed By Attct Pentanucleotide Repeats in Spinocerebellar Ataxia Type 10 Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962