Sodium in PDB 7e4e: uc(Nmr) Solution Structures of Dna Minidumbbell Containing A N1- Methyladenine

The binding sites of Sodium atom in the uc(Nmr) Solution Structures of Dna Minidumbbell Containing A N1- Methyladenine (pdb code 7e4e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the uc(Nmr) Solution Structures of Dna Minidumbbell Containing A N1- Methyladenine, PDB code: 7e4e:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the uc(Nmr) Solution Structures of Dna Minidumbbell Containing A N1- Methyladenine


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 Dna Minidumbbell Containing A N1- Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:0.0 occ:1.00 OP1 A:DT7 2.2 0.0 1.0 OP1 A:DA8 2.2 0.0 1.0 H3' A:DT7 2.5 0.0 1.0 P A:DA8 3.3 0.0 1.0 H5'' A:DT7 3.3 0.0 1.0 O5' A:DA8 3.4 0.0 1.0 C3' A:DT7 3.5 0.0 1.0 P A:DT7 3.6 0.0 1.0 O3' A:DT7 3.8 0.0 1.0 C5' A:DT7 4.0 0.0 1.0 O5' A:DT7 4.1 0.0 1.0 H5' A:DA8 4.1 0.0 1.0 C4' A:DT7 4.3 0.0 1.0 C5' A:DA8 4.3 0.0 1.0 OP2 A:DT7 4.4 0.0 1.0 H2' A:DT7 4.4 0.0 1.0 C2' A:DT7 4.5 0.0 1.0 H4' A:DA8 4.6 0.0 1.0 OP2 A:DA8 4.6 0.0 1.0 H4' A:DT7 4.7 0.0 1.0 O3' A:DT6 4.7 0.0 1.0 H2'' A:DT7 4.9 0.0 1.0 C4' A:DA8 5.0 0.0 1.0

Sodium binding site 2 out of 6 in the uc(Nmr) Solution Structures of Dna Minidumbbell Containing A N1- Methyladenine


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 Dna Minidumbbell Containing A N1- Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.0 occ:1.00 OP1 A:DT2 2.2 0.0 1.0 O4' A:DT2 2.3 0.0 1.0 O5' A:DT2 2.5 0.0 1.0 H5' A:DT2 2.6 0.0 1.0 C5' A:DT2 2.8 0.0 1.0 P A:DT2 2.9 0.0 1.0 N1 A:DT2 3.1 0.0 1.0 C4' A:DT2 3.1 0.0 1.0 C1' A:DT2 3.2 0.0 1.0 C6 A:DT2 3.2 0.0 1.0 H6 A:DT2 3.4 0.0 1.0 H4' A:DT2 3.7 0.0 1.0 C2 A:DT2 3.7 0.0 1.0 O3' A:DT1 3.8 0.0 1.0 H5'' A:DT2 3.9 0.0 1.0 H2' A:DT2 3.9 0.0 1.0 C5 A:DT2 4.0 0.0 1.0 C2' A:DT2 4.0 0.0 1.0 H1' A:DT2 4.1 0.0 1.0 OP2 A:DT2 4.1 0.0 1.0 O2 A:DT2 4.3 0.0 1.0 C3' A:DT2 4.3 0.0 1.0 N3 A:DT2 4.4 0.0 1.0 C4 A:DT2 4.6 0.0 1.0 H73 A:DT2 4.7 0.0 1.0 C7 A:DT2 4.8 0.0 1.0 H72 A:DT2 4.9 0.0 1.0 H3' A:DT2 4.9 0.0 1.0

Sodium binding site 3 out of 6 in the uc(Nmr) Solution Structures of Dna Minidumbbell Containing A N1- Methyladenine


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 Dna Minidumbbell Containing A N1- Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.0 occ:1.00 OP1 A:DT5 2.2 0.0 1.0 OP1 A:MA74 2.2 0.0 1.0 O4' A:MA74 2.4 0.0 1.0 H4' A:MA74 2.5 0.0 1.0 C4' A:MA74 2.9 0.0 1.0 P A:DT5 3.4 0.0 1.0 H5'' A:DT3 3.4 0.0 1.0 P A:MA74 3.5 0.0 1.0 H1' A:MA74 3.5 0.0 1.0 C1' A:MA74 3.6 0.0 1.0 O5' A:DT5 3.6 0.0 1.0 H4' A:DT3 3.7 0.0 1.0 O5' A:MA74 3.8 0.0 1.0 C5' A:MA74 3.9 0.0 1.0 C3' A:MA74 3.9 0.0 1.0 O3' A:MA74 4.0 0.0 1.0 NA A:NA105 4.2 0.0 1.0 C5' A:DT3 4.3 0.0 1.0 H5'' A:MA74 4.4 0.0 1.0 C4' A:DT3 4.4 0.0 1.0 C2' A:MA74 4.4 0.0 1.0 H72 A:DT6 4.4 0.0 1.0 O3' A:DT3 4.4 0.0 1.0 OP2 A:MA74 4.5 0.0 1.0 H5' A:DT3 4.6 0.0 1.0 N9 A:MA74 4.6 0.0 1.0 OP2 A:DT5 4.7 0.0 1.0 H3' A:DT3 4.7 0.0 1.0 H5' A:MA74 4.8 0.0 1.0 C3' A:DT3 4.8 0.0 1.0 H8 A:MA74 4.8 0.0 1.0 H2'' A:MA74 4.8 0.0 1.0 H3' A:MA74 4.8 0.0 1.0 OP1 A:DT3 4.9 0.0 1.0

Sodium binding site 4 out of 6 in the uc(Nmr) Solution Structures of Dna Minidumbbell Containing A N1- Methyladenine


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 Dna Minidumbbell Containing A N1- Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.0 occ:1.00 OP2 A:DA8 2.2 0.0 1.0 O3' A:DT7 2.4 0.0 1.0 N7 A:DA8 2.5 0.0 1.0 H8 A:DA8 2.8 0.0 1.0 P A:DA8 2.9 0.0 1.0 C8 A:DA8 2.9 0.0 1.0 H4' A:DT7 3.5 0.0 1.0 C3' A:DT7 3.6 0.0 1.0 O5' A:DA8 3.6 0.0 1.0 H1' A:DT7 3.7 0.0 1.0 C5 A:DA8 3.7 0.0 1.0 H2'' A:DT7 3.8 0.0 1.0 H5'' A:DA8 3.9 0.0 1.0 C4' A:DT7 4.0 0.0 1.0 H62 A:DA8 4.1 0.0 1.0 C2' A:DT7 4.1 0.0 1.0 N9 A:DA8 4.1 0.0 1.0 OP1 A:DA8 4.2 0.0 1.0 C1' A:DT7 4.3 0.0 1.0 C5' A:DA8 4.3 0.0 1.0 O4' A:DT7 4.4 0.0 1.0 H3' A:DT7 4.4 0.0 1.0 C4 A:DA8 4.5 0.0 1.0 C6 A:DA8 4.5 0.0 1.0 N6 A:DA8 4.7 0.0 1.0 H5' A:DA8 5.0 0.0 1.0

Sodium binding site 5 out of 6 in the uc(Nmr) Solution Structures of Dna Minidumbbell Containing A N1- Methyladenine


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 Dna Minidumbbell Containing A N1- Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:0.0 occ:1.00 OP1 A:DT3 2.2 0.0 1.0 OP2 A:MA74 2.3 0.0 1.0 H3' A:DT3 2.5 0.0 1.0 OP1 A:MA74 2.5 0.0 1.0 P A:MA74 2.8 0.0 1.0 H5'' A:DT3 3.2 0.0 1.0 C3' A:DT3 3.4 0.0 1.0 O3' A:DT3 3.5 0.0 1.0 P A:DT3 3.5 0.0 1.0 C5' A:DT3 3.9 0.0 1.0 O5' A:DT3 4.0 0.0 1.0 C4' A:DT3 4.2 0.0 1.0 NA A:NA103 4.2 0.0 1.0 O5' A:MA74 4.3 0.0 1.0 OP2 A:DT3 4.3 0.0 1.0 H4' A:DT3 4.4 0.0 1.0 H2' A:DT3 4.5 0.0 1.0 C2' A:DT3 4.5 0.0 1.0 O3' A:DT2 4.7 0.0 1.0 H2'' A:DT3 4.9 0.0 1.0 H5' A:DT3 4.9 0.0 1.0

Sodium binding site 6 out of 6 in the uc(Nmr) Solution Structures of Dna Minidumbbell Containing A N1- Methyladenine


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 Dna Minidumbbell Containing A N1- Methyladenine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:0.0 occ:1.00 OP1 A:DT6 2.2 0.0 1.0 O4 A:DT2 2.3 0.0 1.0 O4' A:DT6 2.4 0.0 1.0 H6 A:DT6 2.7 0.0 1.0 H5' A:DT6 3.1 0.0 1.0 C6 A:DT6 3.2 0.0 1.0 C4 A:DT2 3.4 0.0 1.0 C4' A:DT6 3.4 0.0 1.0 C1' A:DT6 3.4 0.0 1.0 N1 A:DT6 3.5 0.0 1.0 P A:DT6 3.5 0.0 1.0 C5' A:DT6 3.6 0.0 1.0 H3 A:DT2 3.7 0.0 1.0 H4' A:DT6 3.8 0.0 1.0 O5' A:DT6 3.9 0.0 1.0 N3 A:DT2 4.0 0.0 1.0 H71 A:DT6 4.0 0.0 1.0 C5 A:DT6 4.1 0.0 1.0 H1' A:DT6 4.1 0.0 1.0 H71 A:DT2 4.2 0.0 1.0 O3' A:DT5 4.2 0.0 1.0 H2' A:DT6 4.3 0.0 1.0 C2' A:DT6 4.4 0.0 1.0 C5 A:DT2 4.5 0.0 1.0 C7 A:DT6 4.5 0.0 1.0 H5'' A:DT6 4.6 0.0 1.0 C3' A:DT6 4.6 0.0 1.0 C2 A:DT6 4.7 0.0 1.0 OP2 A:DT6 4.7 0.0 1.0 C7 A:DT2 4.8 0.0 1.0 H73 A:DT6 4.8 0.0 1.0

L.Wan, S.L.Lam, H.K.Lee, P.Guo. Effects of Adenine Methylation on the Structure and Thermodynamic Stability of A Dna Minidumbbell To Be Published.