Sodium in PDB 7vm9: Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops

The binding sites of Sodium atom in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops (pdb code 7vm9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops, PDB code: 7vm9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:0.0 occ:1.00 OP2 A:DG5 2.6 0.0 1.0 OP1 A:DG5 2.7 0.0 1.0 P A:DG5 3.0 0.0 1.0 O3' A:DT4 3.8 0.0 1.0 O5' A:DG5 4.5 0.0 1.0 H3' A:DT4 4.6 0.0 1.0 C3' A:DT4 4.7 0.0 1.0 NA A:NA108 5.0 0.0 1.0

Sodium binding site 2 out of 9 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.0 occ:1.00 H5'' A:DC6 2.5 0.0 1.0 OP1 A:DC6 2.6 0.0 1.0 H3' A:DC6 2.7 0.0 1.0 OP2 A:DT7 2.7 0.0 1.0 OP1 A:DT7 2.9 0.0 1.0 P A:DT7 3.1 0.0 1.0 C5' A:DC6 3.3 0.0 1.0 C3' A:DC6 3.5 0.0 1.0 O5' A:DC6 3.5 0.0 1.0 P A:DC6 3.6 0.0 1.0 O3' A:DC6 3.8 0.0 1.0 C4' A:DC6 3.9 0.0 1.0 H4' A:DC6 4.1 0.0 1.0 H5' A:DC6 4.2 0.0 1.0 OP2 A:DC6 4.4 0.0 1.0 O5' A:DT7 4.6 0.0 1.0 C2' A:DC6 4.8 0.0 1.0 H2' A:DC6 4.8 0.0 1.0 O3' A:DG5 4.8 0.0 1.0

Sodium binding site 3 out of 9 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.0 occ:1.00 OP2 A:DT2 2.6 0.0 1.0 OP1 A:DT2 2.6 0.0 1.0 P A:DT2 3.0 0.0 1.0 H5'' A:DT2 3.6 0.0 1.0 O5' A:DT2 4.1 0.0 1.0 C5' A:DT2 4.2 0.0 1.0 O3' A:DC1 4.3 0.0 1.0 H5' A:DT2 4.4 0.0 1.0 H3' A:DC1 4.6 0.0 1.0 C3' A:DC1 5.0 0.0 1.0

Sodium binding site 4 out of 9 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.0 occ:1.00 OP2 A:DT9 2.5 0.0 1.0 H3' A:DT9 2.5 0.0 1.0 OP1 A:DG10 2.5 0.0 1.0 O2 A:DT8 2.7 0.0 1.0 H1' A:DT8 3.3 0.0 1.0 C3' A:DT9 3.5 0.0 1.0 H2' A:DT9 3.7 0.0 1.0 H2'' A:DT8 3.8 0.0 1.0 P A:DG10 3.8 0.0 1.0 P A:DT9 3.8 0.0 1.0 C2 A:DT8 3.9 0.0 1.0 C2' A:DT9 4.0 0.0 1.0 O3' A:DT9 4.0 0.0 1.0 H2'' A:DT9 4.2 0.0 1.0 C1' A:DT8 4.2 0.0 1.0 O5' A:DT9 4.2 0.0 1.0 H5'' A:DT9 4.4 0.0 1.0 C2' A:DT8 4.5 0.0 1.0 N1 A:DT8 4.6 0.0 1.0 O5' A:DG10 4.7 0.0 1.0 C4' A:DT9 4.7 0.0 1.0 C5' A:DT9 4.7 0.0 1.0 OP1 A:DT9 4.7 0.0 1.0 H3 A:DT8 4.9 0.0 1.0 N3 A:DT8 4.9 0.0 1.0 OP2 A:DG10 4.9 0.0 1.0 O3' A:DT8 4.9 0.0 1.0

Sodium binding site 5 out of 9 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:0.0 occ:1.00 OP2 A:DG10 2.6 0.0 1.0 O3' A:DT9 2.6 0.0 1.0 O4' A:DG10 2.7 0.0 1.0 P A:DG10 3.2 0.0 1.0 H5'' A:DG10 3.2 0.0 1.0 H1' A:DT9 3.3 0.0 1.0 N9 A:DG10 3.5 0.0 1.0 H2'' A:DT9 3.6 0.0 1.0 C1' A:DG10 3.7 0.0 1.0 C8 A:DG10 3.7 0.0 1.0 C5' A:DG10 3.7 0.0 1.0 C4' A:DG10 3.8 0.0 1.0 H8 A:DG10 3.8 0.0 1.0 C3' A:DT9 3.8 0.0 1.0 O5' A:DG10 3.9 0.0 1.0 H4' A:DT9 3.9 0.0 1.0 C2' A:DT9 4.1 0.0 1.0 C4 A:DG10 4.1 0.0 1.0 C1' A:DT9 4.1 0.0 1.0 O2 A:DT9 4.2 0.0 1.0 N7 A:DG10 4.3 0.0 1.0 C4' A:DT9 4.4 0.0 1.0 H1' A:DG10 4.4 0.0 1.0 OP1 A:DG10 4.5 0.0 1.0 C5 A:DG10 4.5 0.0 1.0 H4' A:DG10 4.5 0.0 1.0 H2' A:DG10 4.5 0.0 1.0 C2' A:DG10 4.6 0.0 1.0 C3' A:DG10 4.6 0.0 1.0 H3' A:DG10 4.6 0.0 1.0 H3' A:DT9 4.7 0.0 1.0 N3 A:DG10 4.8 0.0 1.0 H5' A:DG10 4.8 0.0 1.0 O4' A:DT9 4.9 0.0 1.0

Sodium binding site 6 out of 9 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:0.0 occ:1.00 H1' A:DT4 2.6 0.0 1.0 O2 A:DT3 2.6 0.0 1.0 O6 A:DG5 2.6 0.0 1.0 O2 A:DT4 2.6 0.0 1.0 N7 A:DG5 2.8 0.0 1.0 O4' A:DT4 2.9 0.0 1.0 C6 A:DG5 3.0 0.0 1.0 C5 A:DG5 3.1 0.0 1.0 C1' A:DT4 3.1 0.0 1.0 C2 A:DT4 3.3 0.0 1.0 N1 A:DT4 3.6 0.0 1.0 C2 A:DT3 3.7 0.0 1.0 H41 A:DC1 3.7 0.0 1.0 H3 A:DT3 3.8 0.0 1.0 C8 A:DG5 3.9 0.0 1.0 C4' A:DT4 4.2 0.0 1.0 N1 A:DG5 4.2 0.0 1.0 H4' A:DT4 4.2 0.0 1.0 N3 A:DT3 4.2 0.0 1.0 C4 A:DG5 4.3 0.0 1.0 H1' A:DT3 4.3 0.0 1.0 H8 A:DG5 4.4 0.0 1.0 N3 A:DT4 4.4 0.0 1.0 C2' A:DT4 4.5 0.0 1.0 H1 A:DG5 4.6 0.0 1.0 H2'' A:DT4 4.6 0.0 1.0 N4 A:DC1 4.7 0.0 1.0 N9 A:DG5 4.7 0.0 1.0 H3 A:DT4 4.7 0.0 1.0 C6 A:DT4 4.8 0.0 1.0 N1 A:DT3 4.8 0.0 1.0 H5' A:DT4 4.9 0.0 1.0

Sodium binding site 7 out of 9 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:0.0 occ:1.00 OP1 A:DT8 2.5 0.0 1.0 H1' A:DT7 2.6 0.0 1.0 O2 A:DT7 2.7 0.0 1.0 O4' A:DT7 2.7 0.0 1.0 C1' A:DT7 3.1 0.0 1.0 C2 A:DT7 3.4 0.0 1.0 H4' A:DT7 3.6 0.0 1.0 N1 A:DT7 3.6 0.0 1.0 C4' A:DT7 3.7 0.0 1.0 P A:DT8 3.9 0.0 1.0 H5'' A:DT8 4.4 0.0 1.0 C2' A:DT7 4.4 0.0 1.0 C3' A:DT7 4.5 0.0 1.0 O3' A:DT7 4.6 0.0 1.0 N3 A:DT7 4.6 0.0 1.0 OP2 A:DT8 4.8 0.0 1.0 H2'' A:DT7 4.8 0.0 1.0 O5' A:DT8 4.9 0.0 1.0 H5' A:DT7 4.9 0.0 1.0 H3 A:DT7 4.9 0.0 1.0 C6 A:DT7 4.9 0.0 1.0 C5' A:DT7 4.9 0.0 1.0 H5' A:DT8 4.9 0.0 1.0 C5' A:DT8 5.0 0.0 1.0

Sodium binding site 8 out of 9 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:0.0 occ:1.00 OP1 A:DT4 2.4 0.0 1.0 OP1 A:DG5 2.6 0.0 1.0 O5' A:DG5 2.7 0.0 1.0 H5'' A:DT4 3.0 0.0 1.0 P A:DG5 3.2 0.0 1.0 H4' A:DG5 3.5 0.0 1.0 H3' A:DT4 3.8 0.0 1.0 P A:DT4 3.8 0.0 1.0 C5' A:DG5 3.9 0.0 1.0 C5' A:DT4 3.9 0.0 1.0 C4' A:DG5 4.1 0.0 1.0 O5' A:DT4 4.1 0.0 1.0 H5' A:DG5 4.3 0.0 1.0 O3' A:DT4 4.3 0.0 1.0 OP2 A:DG5 4.3 0.0 1.0 C3' A:DT4 4.4 0.0 1.0 O4' A:DG5 4.4 0.0 1.0 C4' A:DT4 4.7 0.0 1.0 O3' A:DT3 4.7 0.0 1.0 H5'' A:DG5 4.7 0.0 1.0 H5' A:DT4 4.7 0.0 1.0 H4' A:DT4 4.8 0.0 1.0 OP2 A:DT4 4.9 0.0 1.0 NA A:NA101 5.0 0.0 1.0

Sodium binding site 9 out of 9 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Solution uc(Nmr) Structures of Dna Minidumbbell Formed with Two Regular Ctttg Pentaloops within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:0.0 occ:1.00 H3' A:DT3 2.4 0.0 1.0 OP2 A:DT3 2.5 0.0 1.0 H2' A:DT3 3.0 0.0 1.0 C3' A:DT3 3.4 0.0 1.0 C2' A:DT3 3.6 0.0 1.0 P A:DT3 3.7 0.0 1.0 O5' A:DT3 3.7 0.0 1.0 OP2 A:DT4 3.9 0.0 1.0 H2'' A:DT3 3.9 0.0 1.0 H5'' A:DT3 4.1 0.0 1.0 O3' A:DT3 4.1 0.0 1.0 C5' A:DT3 4.3 0.0 1.0 C4' A:DT3 4.4 0.0 1.0 H6 A:DT3 4.6 0.0 1.0 O3' A:DT2 4.7 0.0 1.0 P A:DT4 4.7 0.0 1.0 OP1 A:DT3 4.7 0.0 1.0 H71 A:DT4 4.8 0.0 1.0 C1' A:DT3 5.0 0.0 1.0

C.K.Ngai, S.L.Lam, H.K.Lee, P.Guo. A Purine and A Backbone Discontinuous Site Alter the Structure and Thermal Stability of Dna Minidumbbells Containing Two Pentaloops. Febs Lett. V. 596 826 2022.
ISSN: ISSN 0014-5793
PubMed: 35060128
DOI: 10.1002/1873-3468.14293