Sodium in PDB 1ply: Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)

The binding sites of Sodium atom in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) (pdb code 1ply). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T), PDB code: 1ply:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) within 5.0Å range:

Sodium binding site 2 out of 10 in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7 b:4.0 occ:1.00 O A:HOH14 2.6 4.0 1.0 OP1 A:DA2 2.8 4.0 1.0 H3' A:DA1 3.1 4.0 1.0 OP2 A:DA2 3.2 4.0 1.0 P A:DA2 3.5 4.0 1.0 H5'' A:DA1 3.7 4.0 1.0 C3' A:DA1 4.0 4.0 1.0 O3' A:DA1 4.2 4.0 1.0 O5' A:DA1 4.3 4.0 1.0 C5' A:DA1 4.4 4.0 1.0 C4' A:DA1 4.6 4.0 1.0 H4' A:DA1 4.7 4.0 1.0 O5' A:DA2 4.9 4.0 1.0

Sodium binding site 3 out of 10 in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8 b:4.0 occ:1.00 O A:HOH15 2.8 4.0 1.0 OP1 A:DA1 2.9 4.0 1.0 H2' A:DA1 3.3 4.0 1.0 P A:DA1 4.1 4.0 1.0 O5' A:DA1 4.2 4.0 1.0 H8 A:DA1 4.2 4.0 1.0 C2' A:DA1 4.2 4.0 1.0 NA A:NA9 4.3 4.0 1.0 H2'' A:DA1 4.4 4.0 1.0 O A:HOH14 4.6 4.0 1.0 H3' A:DA1 4.7 4.0 1.0 C3' A:DA1 5.0 4.0 1.0

Sodium binding site 4 out of 10 in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na9 b:4.0 occ:1.00 O A:HOH15 2.9 4.0 1.0 NA A:NA8 4.3 4.0 1.0

Sodium binding site 5 out of 10 in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na10 b:4.0 occ:1.00 O A:HOH16 3.9 4.0 1.0 H2'' A:DA2 3.9 4.0 1.0 H8 A:DA3 4.3 4.0 1.0 H2' A:DA2 4.5 4.0 1.0 C2' A:DA2 4.7 4.0 1.0

Sodium binding site 6 out of 10 in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:4.0 occ:1.00 H72 B:DT10 2.7 4.0 1.0 O4 B:DT10 3.3 4.0 1.0 C7 B:DT10 3.7 4.0 1.0 H73 B:DT10 3.8 4.0 1.0 C4 B:DT10 4.0 4.0 1.0 C5 B:DT10 4.3 4.0 1.0 H61 A:DA1 4.4 4.0 1.0 H71 B:DT10 4.5 4.0 1.0 H72 B:DT9 4.8 4.0 1.0

Sodium binding site 7 out of 10 in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:4.0 occ:1.00 H71 B:DT10 2.7 4.0 1.0 OP2 B:DT10 3.1 4.0 1.0 H2'' B:DT9 3.2 4.0 1.0 C7 B:DT10 3.7 4.0 1.0 H6 B:DT10 3.8 4.0 1.0 H72 B:DT10 3.9 4.0 1.0 O B:HOH21 3.9 4.0 1.0 C2' B:DT9 3.9 4.0 1.0 H2' B:DT9 4.0 4.0 1.0 H3' B:DT9 4.0 4.0 1.0 H73 B:DT10 4.3 4.0 1.0 C3' B:DT9 4.4 4.0 1.0 P B:DT10 4.5 4.0 1.0 C6 B:DT10 4.5 4.0 1.0 H2' B:DT10 4.6 4.0 1.0 C5 B:DT10 4.6 4.0 1.0 O3' B:DT9 4.7 4.0 1.0

Sodium binding site 8 out of 10 in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na11 b:4.0 occ:1.00 O A:HOH16 3.1 4.0 1.0

Sodium binding site 9 out of 10 in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na12 b:4.0 occ:1.00 OP1 B:DT9 3.2 4.0 1.0 H5'' B:DT9 3.3 4.0 1.0 H5' B:DT9 3.8 4.0 1.0 C5' B:DT9 4.0 4.0 1.0 P B:DT9 4.3 4.0 1.0 O5' B:DT9 4.3 4.0 1.0 O3' B:DT8 4.7 4.0 1.0 H4' B:DT8 4.7 4.0 1.0

Sodium binding site 10 out of 10 in the Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Sodium Ions and Water Molecules in the Structure of Poly D(A)(Dot)Poly D(T) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na13 b:4.0 occ:1.00 OP2 B:DT7 3.1 4.0 1.0 O B:HOH23 3.2 4.0 1.0 H2' B:DT7 4.3 4.0 1.0 P B:DT7 4.5 4.0 1.0 H71 B:DT7 4.7 4.0 1.0 H6 B:DT7 4.7 4.0 1.0 O5' B:DT7 4.8 4.0 1.0 H73 B:DT8 4.9 4.0 1.0 H2'' B:DT6 4.9 4.0 1.0 H71 B:DT8 4.9 4.0 1.0

R.Chandrasekaran, A.Radha, H.S.Park. Sodium Ions and Water Molecules in the Structure of Poly(Da).Poly(Dt). Acta Crystallogr.,Sect.D V. 51 1025 1995.
ISSN: ISSN 0907-4449
PubMed: 15299771
DOI: 10.1107/S0907444995001880