Sodium in PDB 5gwl: Structure of Two Cctg Repeats

The binding sites of Sodium atom in the Structure of Two Cctg Repeats (pdb code 5gwl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of Two Cctg Repeats, PDB code: 5gwl:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Structure of Two Cctg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Two Cctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:0.0 occ:1.00 OP1 A:DG4 2.2 0.0 1.0 OP1 A:DT3 2.2 0.0 1.0 OP2 A:DT3 2.6 0.0 1.0 P A:DT3 2.7 0.0 1.0 O5' A:DT3 3.1 0.0 1.0 H5'' A:DT3 3.3 0.0 1.0 H3' A:DT3 3.5 0.0 1.0 P A:DG4 3.5 0.0 1.0 C5' A:DT3 3.7 0.0 1.0 O5' A:DG4 4.0 0.0 1.0 C3' A:DT3 4.2 0.0 1.0 O3' A:DC2 4.3 0.0 1.0 O3' A:DT3 4.4 0.0 1.0 C4' A:DT3 4.6 0.0 1.0 H5' A:DT3 4.6 0.0 1.0 OP2 A:DG4 4.7 0.0 1.0 H6 A:DT3 5.0 0.0 1.0

Sodium binding site 2 out of 7 in the Structure of Two Cctg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Two Cctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.0 occ:1.00 OP2 A:DT7 2.2 0.0 1.0 OP1 A:DT7 2.3 0.0 1.0 P A:DT7 2.7 0.0 1.0 O5' A:DT7 3.7 0.0 1.0 O3' A:DC6 4.0 0.0 1.0 H4' A:DC6 4.1 0.0 1.0 H5'' A:DT7 4.3 0.0 1.0 C5' A:DT7 4.5 0.0 1.0 H5' A:DT7 4.6 0.0 1.0 C4' A:DC6 5.0 0.0 1.0

Sodium binding site 3 out of 7 in the Structure of Two Cctg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Two Cctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.0 occ:1.00 OP2 A:DC2 2.3 0.0 1.0 OP1 A:DC2 2.3 0.0 1.0 P A:DC2 2.7 0.0 1.0 H5'' A:DC2 3.8 0.0 1.0 O5' A:DC2 3.9 0.0 1.0 O3' A:DC1 3.9 0.0 1.0 H5' A:DC2 4.1 0.0 1.0 C5' A:DC2 4.2 0.0 1.0 H3' A:DC1 4.4 0.0 1.0 HO5' A:DC1 4.7 0.0 1.0 C3' A:DC1 4.7 0.0 1.0

Sodium binding site 4 out of 7 in the Structure of Two Cctg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Two Cctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.0 occ:1.00 OP2 A:DG4 2.2 0.0 1.0 O3' A:DT3 2.4 0.0 1.0 P A:DG4 2.9 0.0 1.0 H2'' A:DT3 3.4 0.0 1.0 H5'' A:DG4 3.4 0.0 1.0 C3' A:DT3 3.6 0.0 1.0 C2' A:DT3 3.8 0.0 1.0 H2' A:DT3 3.9 0.0 1.0 OP1 A:DG4 3.9 0.0 1.0 O5' A:DG4 4.0 0.0 1.0 H3' A:DT3 4.1 0.0 1.0 C5' A:DG4 4.2 0.0 1.0 H4' A:DT3 4.6 0.0 1.0 H5' A:DG4 4.6 0.0 1.0 C4' A:DT3 4.8 0.0 1.0

Sodium binding site 5 out of 7 in the Structure of Two Cctg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Two Cctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:0.0 occ:1.00 OP2 A:DG8 2.2 0.0 1.0 O2 A:DC6 2.3 0.0 1.0 H22 A:DG8 2.4 0.0 1.0 N3 A:DC2 2.5 0.0 1.0 N2 A:DG8 2.5 0.0 1.0 N3 A:DC6 2.6 0.0 1.0 C2 A:DC6 2.8 0.0 1.0 H21 A:DG8 2.9 0.0 1.0 O2 A:DC2 2.9 0.0 1.0 C2 A:DC2 3.1 0.0 1.0 C2 A:DG8 3.2 0.0 1.0 H42 A:DC2 3.2 0.0 1.0 H4' A:DT7 3.5 0.0 1.0 P A:DG8 3.5 0.0 1.0 C4 A:DC2 3.5 0.0 1.0 N3 A:DG8 3.5 0.0 1.0 H42 A:DC6 3.6 0.0 1.0 O5' A:DG8 3.7 0.0 1.0 N4 A:DC2 3.7 0.0 1.0 C4 A:DC6 3.8 0.0 1.0 O2 A:DC5 4.0 0.0 1.0 H1' A:DT7 4.1 0.0 1.0 N1 A:DC6 4.2 0.0 1.0 N4 A:DC6 4.2 0.0 1.0 N1 A:DG8 4.2 0.0 1.0 H2'' A:DC6 4.4 0.0 1.0 H1 A:DG8 4.4 0.0 1.0 C4' A:DT7 4.4 0.0 1.0 N1 A:DC2 4.4 0.0 1.0 O3' A:DT7 4.5 0.0 1.0 OP1 A:DG8 4.5 0.0 1.0 O4' A:DT7 4.7 0.0 1.0 H41 A:DC2 4.7 0.0 1.0 C4 A:DG8 4.7 0.0 1.0 H22 A:DG4 4.7 0.0 1.0 H1' A:DC6 4.8 0.0 1.0 O4' A:DG8 4.8 0.0 1.0 H21 A:DG4 4.8 0.0 1.0 C5 A:DC2 4.8 0.0 1.0 N2 A:DG4 4.8 0.0 1.0 C1' A:DC6 4.9 0.0 1.0 C1' A:DT7 4.9 0.0 1.0 H2' A:DC6 4.9 0.0 1.0 C5 A:DC6 4.9 0.0 1.0 C2' A:DC6 5.0 0.0 1.0

Sodium binding site 6 out of 7 in the Structure of Two Cctg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Two Cctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:0.0 occ:1.00 OP1 A:DC5 2.1 0.0 1.0 OP1 A:DC6 2.3 0.0 1.0 OP2 A:DC6 2.3 0.0 1.0 P A:DC6 2.7 0.0 1.0 H4' A:DC5 2.9 0.0 1.0 H5' A:DC5 3.3 0.0 1.0 P A:DC5 3.6 0.0 1.0 C4' A:DC5 3.7 0.0 1.0 O3' A:DC5 3.8 0.0 1.0 C5' A:DC5 3.8 0.0 1.0 O5' A:DC6 3.9 0.0 1.0 C3' A:DC5 4.1 0.0 1.0 O5' A:DC5 4.2 0.0 1.0 H3' A:DC5 4.3 0.0 1.0 O3' A:DG4 4.3 0.0 1.0 OP2 A:DC5 4.7 0.0 1.0 H5'' A:DC5 4.9 0.0 1.0 H5'' A:DC6 4.9 0.0 1.0 O4' A:DC5 4.9 0.0 1.0 C5' A:DC6 5.0 0.0 1.0

Sodium binding site 7 out of 7 in the Structure of Two Cctg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Two Cctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:0.0 occ:1.00 OP1 A:DG8 2.2 0.0 1.0 O2 A:DT7 2.2 0.0 1.0 O6 A:DG8 2.3 0.0 1.0 C6 A:DG8 2.7 0.0 1.0 H2'' A:DT7 2.9 0.0 1.0 C5 A:DG8 3.2 0.0 1.0 H1' A:DT7 3.4 0.0 1.0 N1 A:DG8 3.4 0.0 1.0 C2 A:DT7 3.4 0.0 1.0 H41 A:DC5 3.6 0.0 1.0 P A:DG8 3.6 0.0 1.0 H1 A:DG8 3.6 0.0 1.0 N7 A:DG8 3.6 0.0 1.0 C2' A:DT7 3.8 0.0 1.0 C1' A:DT7 3.9 0.0 1.0 H5'' A:DG8 4.0 0.0 1.0 N1 A:DT7 4.2 0.0 1.0 C4 A:DG8 4.2 0.0 1.0 O3' A:DT7 4.3 0.0 1.0 OP2 A:DG8 4.3 0.0 1.0 C2 A:DG8 4.3 0.0 1.0 N4 A:DC5 4.4 0.0 1.0 H3 A:DT7 4.4 0.0 1.0 N3 A:DT7 4.5 0.0 1.0 H2' A:DT7 4.6 0.0 1.0 N3 A:DC5 4.6 0.0 1.0 C8 A:DG8 4.6 0.0 1.0 O5' A:DG8 4.7 0.0 1.0 C3' A:DT7 4.7 0.0 1.0 N3 A:DG8 4.8 0.0 1.0 C5' A:DG8 4.8 0.0 1.0 N9 A:DG8 4.9 0.0 1.0 C4 A:DC5 5.0 0.0 1.0

P.Guo, S.L.Lam. Minidumbbell: A New Form of Native Dna Structure J.Am.Chem.Soc. V. 138 12534 2016.
ISSN: ESSN 1520-5126
PubMed: 27589409
DOI: 10.1021/JACS.6B06897