Sodium in PDB 7yf7: uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Atttt Repeats

The binding sites of Sodium atom in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Atttt Repeats (pdb code 7yf7). 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 the Dna Minidumbbell Formed By Two Atttt Repeats, PDB code: 7yf7:
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 the Dna Minidumbbell Formed By Two Atttt 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 Structures of the Dna Minidumbbell Formed By Two Atttt Repeats 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 OP1 A:DT5 2.3 0.0 1.0 OP2 A:DT5 2.5 0.0 1.0 H5' A:DT7 2.6 0.0 1.0 O5' A:DT7 2.7 0.0 1.0 H4' A:DA6 2.8 0.0 1.0 P A:DT5 2.8 0.0 1.0 O4' A:DA6 2.9 0.0 1.0 P A:DT7 3.1 0.0 1.0 C5' A:DT7 3.1 0.0 1.0 C4' A:DA6 3.3 0.0 1.0 H1' A:DA6 3.5 0.0 1.0 H5'' A:DT7 3.5 0.0 1.0 O5' A:DT5 3.7 0.0 1.0 C1' A:DA6 3.8 0.0 1.0 O3' A:DA6 4.0 0.0 1.0 C3' A:DA6 4.1 0.0 1.0 NA A:NA105 4.1 0.0 1.0 O3' A:DT4 4.3 0.0 1.0 OP2 A:DT7 4.3 0.0 1.0 C4' A:DT7 4.4 0.0 1.0 O5' A:DA6 4.4 0.0 1.0 H5'' A:DT5 4.5 0.0 1.0 C2' A:DA6 4.5 0.0 1.0 C5' A:DA6 4.5 0.0 1.0 H2'' A:DA6 4.6 0.0 1.0 O4' A:DT7 4.7 0.0 1.0 C5' A:DT5 4.7 0.0 1.0 H4' A:DT4 4.7 0.0 1.0 H3' A:DT4 4.8 0.0 1.0 H4' A:DT7 4.9 0.0 1.0 H71 A:DT8 4.9 0.0 1.0 H4' A:DT5 5.0 0.0 1.0 C3' A:DT4 5.0 0.0 1.0

Sodium binding site 2 out of 9 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Atttt 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 Structures of the Dna Minidumbbell Formed By Two Atttt Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.0 occ:1.00 OP1 A:DT8 2.3 0.0 1.0 O2 A:DT8 2.4 0.0 1.0 O4' A:DT8 2.5 0.0 1.0 H5' A:DT8 2.9 0.0 1.0 C2 A:DT8 3.1 0.0 1.0 C4' A:DT8 3.4 0.0 1.0 C5' A:DT8 3.5 0.0 1.0 H4' A:DT8 3.5 0.0 1.0 P A:DT8 3.6 0.0 1.0 C1' A:DT8 3.6 0.0 1.0 N1 A:DT8 3.7 0.0 1.0 N3 A:DT8 3.8 0.0 1.0 H3 A:DT8 3.9 0.0 1.0 O5' A:DT8 3.9 0.0 1.0 H1' A:DT8 4.0 0.0 1.0 O3' A:DT7 4.1 0.0 1.0 H5'' A:DT8 4.5 0.0 1.0 C3' A:DT8 4.7 0.0 1.0 C2' A:DT8 4.8 0.0 1.0 OP2 A:DT8 4.8 0.0 1.0 C6 A:DT8 5.0 0.0 1.0

Sodium binding site 3 out of 9 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Atttt 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 Structures of the Dna Minidumbbell Formed By Two Atttt Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.0 occ:1.00 O3' A:DT2 2.4 0.0 1.0 OP2 A:DT2 2.4 0.0 1.0 OP2 A:DT3 2.7 0.0 1.0 P A:DT3 3.0 0.0 1.0 H5'' A:DT2 3.2 0.0 1.0 H3' A:DT2 3.3 0.0 1.0 C3' A:DT2 3.3 0.0 1.0 P A:DT2 3.5 0.0 1.0 OP1 A:DT3 3.6 0.0 1.0 OP1 A:DT2 3.9 0.0 1.0 C5' A:DT2 3.9 0.0 1.0 C4' A:DT2 4.1 0.0 1.0 O5' A:DT2 4.2 0.0 1.0 O5' A:DT3 4.5 0.0 1.0 H4' A:DT2 4.6 0.0 1.0 C2' A:DT2 4.6 0.0 1.0 H2' A:DT2 4.8 0.0 1.0 O3' A:DA1 4.9 0.0 1.0 H5' A:DT2 4.9 0.0 1.0 H2'' A:DT2 4.9 0.0 1.0 H2'' A:DA1 5.0 0.0 1.0

Sodium binding site 4 out of 9 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Atttt 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 Structures of the Dna Minidumbbell Formed By Two Atttt Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.0 occ:1.00 OP2 A:DT9 2.3 0.0 1.0 OP1 A:DT10 2.3 0.0 1.0 H3' A:DT9 2.8 0.0 1.0 P A:DT10 3.2 0.0 1.0 O3' A:DT9 3.4 0.0 1.0 P A:DT9 3.4 0.0 1.0 C3' A:DT9 3.5 0.0 1.0 O5' A:DT9 3.7 0.0 1.0 OP2 A:DT10 3.7 0.0 1.0 H5'' A:DT9 3.8 0.0 1.0 OP1 A:DT9 4.0 0.0 1.0 NA A:NA106 4.0 0.0 1.0 C5' A:DT9 4.2 0.0 1.0 C4' A:DT9 4.4 0.0 1.0 O5' A:DT10 4.7 0.0 1.0 H2' A:DT9 4.7 0.0 1.0 C2' A:DT9 4.7 0.0 1.0 O3' A:DT8 4.8 0.0 1.0 H4' A:DT9 5.0 0.0 1.0

Sodium binding site 5 out of 9 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Atttt 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 Structures of the Dna Minidumbbell Formed By Two Atttt Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:0.0 occ:1.00 OP1 A:DA6 2.3 0.0 1.0 OP2 A:DT5 2.4 0.0 1.0 O5' A:DT5 2.5 0.0 1.0 O5' A:DA6 2.6 0.0 1.0 H3' A:DT5 2.9 0.0 1.0 P A:DA6 3.1 0.0 1.0 P A:DT5 3.1 0.0 1.0 C3' A:DT5 3.7 0.0 1.0 H4' A:DA6 3.7 0.0 1.0 C5' A:DT5 3.8 0.0 1.0 O3' A:DT5 3.9 0.0 1.0 C5' A:DA6 3.9 0.0 1.0 O3' A:DT4 4.0 0.0 1.0 H4' A:DT5 4.0 0.0 1.0 O4' A:DA6 4.1 0.0 1.0 C4' A:DT5 4.1 0.0 1.0 NA A:NA101 4.1 0.0 1.0 C4' A:DA6 4.1 0.0 1.0 OP1 A:DT5 4.3 0.0 1.0 H5' A:DT5 4.3 0.0 1.0 OP2 A:DA6 4.3 0.0 1.0 H5' A:DA6 4.4 0.0 1.0 H5'' A:DT5 4.5 0.0 1.0 H5'' A:DA6 4.6 0.0 1.0

Sodium binding site 6 out of 9 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Atttt 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 Structures of the Dna Minidumbbell Formed By Two Atttt Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:0.0 occ:1.00 H5'' A:DT9 2.2 0.0 1.0 OP1 A:DT9 2.4 0.0 1.0 OP1 A:DT10 2.5 0.0 1.0 O4 A:DT3 2.5 0.0 1.0 C5' A:DT9 3.2 0.0 1.0 P A:DT9 3.4 0.0 1.0 H5' A:DT9 3.6 0.0 1.0 P A:DT10 3.7 0.0 1.0 O5' A:DT9 3.7 0.0 1.0 H1' A:DT8 3.7 0.0 1.0 C4 A:DT3 3.7 0.0 1.0 O5' A:DT10 3.7 0.0 1.0 H73 A:DT3 3.8 0.0 1.0 OP2 A:DT9 3.9 0.0 1.0 NA A:NA104 4.0 0.0 1.0 H71 A:DT3 4.1 0.0 1.0 C4' A:DT9 4.2 0.0 1.0 H4' A:DT9 4.3 0.0 1.0 C7 A:DT3 4.4 0.0 1.0 C5 A:DT3 4.6 0.0 1.0 H2'' A:DT8 4.6 0.0 1.0 H3' A:DT9 4.6 0.0 1.0 H3 A:DT3 4.6 0.0 1.0 N3 A:DT3 4.7 0.0 1.0 O3' A:DT9 4.7 0.0 1.0 C3' A:DT9 4.7 0.0 1.0 OP2 A:DT10 4.7 0.0 1.0 C1' A:DT8 4.7 0.0 1.0 O3' A:DT8 4.8 0.0 1.0

Sodium binding site 7 out of 9 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Atttt 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 Structures of the Dna Minidumbbell Formed By Two Atttt Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:0.0 occ:1.00 OP2 A:DT8 2.3 0.0 1.0 OP2 A:DT7 2.3 0.0 1.0 H3' A:DT7 2.7 0.0 1.0 H5'' A:DT7 3.6 0.0 1.0 P A:DT8 3.6 0.0 1.0 C3' A:DT7 3.7 0.0 1.0 P A:DT7 3.7 0.0 1.0 O3' A:DT7 3.9 0.0 1.0 C5' A:DT7 4.3 0.0 1.0 O5' A:DT7 4.3 0.0 1.0 OP1 A:DT8 4.5 0.0 1.0 H2' A:DT7 4.5 0.0 1.0 C4' A:DT7 4.6 0.0 1.0 O3' A:DA6 4.6 0.0 1.0 C2' A:DT7 4.7 0.0 1.0 O5' A:DT8 4.7 0.0 1.0 OP1 A:DT7 4.8 0.0 1.0

Sodium binding site 8 out of 9 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Atttt 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 Structures of the Dna Minidumbbell Formed By Two Atttt Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:0.0 occ:1.00 OP1 A:DT2 2.3 0.0 1.0 H1' A:DT10 2.5 0.0 1.0 O3' A:DT10 2.5 0.0 1.0 O4' A:DT10 2.5 0.0 1.0 C1' A:DT10 3.0 0.0 1.0 H4' A:DT10 3.0 0.0 1.0 O3' A:DA1 3.0 0.0 1.0 C4' A:DT10 3.1 0.0 1.0 P A:DT2 3.1 0.0 1.0 C3' A:DT10 3.2 0.0 1.0 HO3' A:DT10 3.3 0.0 1.0 C2' A:DT10 3.6 0.0 1.0 O5' A:DT2 3.7 0.0 1.0 H4' A:DA1 3.7 0.0 1.0 H2'' A:DT10 3.8 0.0 1.0 O2 A:DT10 4.0 0.0 1.0 H3' A:DT10 4.2 0.0 1.0 N1 A:DT10 4.2 0.0 1.0 C3' A:DA1 4.3 0.0 1.0 C4' A:DA1 4.4 0.0 1.0 OP2 A:DT2 4.5 0.0 1.0 C2 A:DT10 4.5 0.0 1.0 H1' A:DA1 4.6 0.0 1.0 C5' A:DT10 4.6 0.0 1.0 O4' A:DA1 4.6 0.0 1.0 H2' A:DT10 4.6 0.0 1.0 C5' A:DT2 4.7 0.0 1.0 H5'' A:DT2 4.8 0.0 1.0 H5' A:DT2 4.8 0.0 1.0 H5'' A:DT10 4.9 0.0 1.0 H5' A:DT10 5.0 0.0 1.0

Sodium binding site 9 out of 9 in the uc(Nmr) Solution Structures of the Dna Minidumbbell Formed By Two Atttt Repeats


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 the Dna Minidumbbell Formed By Two Atttt Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:0.0 occ:1.00 OP1 A:DT4 2.3 0.0 1.0 O4 A:DT8 2.4 0.0 1.0 OP2 A:DT4 2.9 0.0 1.0 P A:DT4 3.0 0.0 1.0 H5'' A:DT4 3.5 0.0 1.0 C4 A:DT8 3.6 0.0 1.0 H3' A:DT4 4.0 0.0 1.0 H1' A:DT3 4.0 0.0 1.0 H71 A:DT8 4.1 0.0 1.0 O5' A:DT4 4.1 0.0 1.0 H73 A:DT8 4.2 0.0 1.0 O3' A:DT3 4.3 0.0 1.0 C5' A:DT4 4.3 0.0 1.0 H3 A:DT8 4.4 0.0 1.0 C7 A:DT8 4.5 0.0 1.0 N3 A:DT8 4.5 0.0 1.0 C5 A:DT8 4.6 0.0 1.0 O2 A:DT3 4.9 0.0 1.0 H5' A:DT7 4.9 0.0 1.0 H2'' A:DT3 4.9 0.0 1.0

J.Li, L.Wan, Y.Wang, Y.Chen, H.K.Lee, S.L.Lam, P.Guo. Solution Nuclear Magnetic Resonance Structures of Atttt and Atttc Pentanucleotide Repeats Associated with SCA37 and Fames. Acs Chem Neurosci 2022.
ISSN: ESSN 1948-7193
PubMed: 36580663
DOI: 10.1021/ACSCHEMNEURO.2C00593