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Sodium in PDB 6m6k: uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg Repeats

Sodium Binding Sites:

The binding sites of Sodium atom in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg Repeats (pdb code 6m6k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg Repeats, PDB code: 6m6k:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 6m6k

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Sodium binding site 1 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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
H3' A:DT3 2.8 0.0 1.0
H5'' A:DT3 3.2 0.0 1.0
P A:DG4 3.5 0.0 1.0
P A:DT3 3.6 0.0 1.0
C3' A:DT3 3.8 0.0 1.0
O5' A:DG4 4.0 0.0 1.0
C5' A:DT3 4.1 0.0 1.0
O3' A:DT3 4.1 0.0 1.0
O5' A:DT3 4.3 0.0 1.0
C4' A:DT3 4.5 0.0 1.0
OP2 A:DT3 4.5 0.0 1.0
O3' A:DC2 4.6 0.0 1.0
OP2 A:DG4 4.8 0.0 1.0
H2' A:DT3 4.8 0.0 1.0
H4' A:DT3 4.9 0.0 1.0
C2' A:DT3 4.9 0.0 1.0
H5' A:DT3 5.0 0.0 1.0

Sodium binding site 2 out of 8 in 6m6k

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Sodium binding site 2 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg Repeats within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na102

b:0.0
occ:1.00
OP1 A:3DR5 2.2 0.0 1.0
OP1 A:DC6 2.2 0.0 1.0
H5' A:3DR5 3.0 0.0 1.0
H4'1 A:3DR5 3.2 0.0 1.0
P A:3DR5 3.3 0.0 1.0
O3' A:DG4 3.3 0.0 1.0
P A:DC6 3.6 0.0 1.0
C5' A:3DR5 3.7 0.0 1.0
H3' A:3DR5 3.8 0.0 1.0
C4' A:3DR5 3.8 0.0 1.0
H5' A:DC6 3.9 0.0 1.0
O5' A:DC6 3.9 0.0 1.0
O5' A:3DR5 4.0 0.0 1.0
C3' A:3DR5 4.2 0.0 1.0
H5'' A:DC6 4.3 0.0 1.0
C5' A:DC6 4.3 0.0 1.0
O3' A:3DR5 4.4 0.0 1.0
H2'' A:DG4 4.6 0.0 1.0
OP2 A:3DR5 4.6 0.0 1.0
C3' A:DG4 4.7 0.0 1.0
H5'' A:3DR5 4.7 0.0 1.0
OP2 A:DC6 4.7 0.0 1.0

Sodium binding site 3 out of 8 in 6m6k

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Sodium binding site 3 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg Repeats within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na103

b:0.0
occ:1.00
OP1 A:DT8 2.2 0.0 1.0
OP1 A:DG9 2.2 0.0 1.0
H3' A:DT8 2.6 0.0 1.0
H5'' A:DT8 3.1 0.0 1.0
P A:DG9 3.6 0.0 1.0
C3' A:DT8 3.6 0.0 1.0
P A:DT8 3.6 0.0 1.0
C5' A:DT8 4.0 0.0 1.0
O3' A:DT8 4.0 0.0 1.0
O5' A:DT8 4.2 0.0 1.0
C4' A:DT8 4.3 0.0 1.0
O5' A:DG9 4.5 0.0 1.0
O3' A:DC7 4.6 0.0 1.0
OP2 A:DG9 4.6 0.0 1.0
OP2 A:DT8 4.6 0.0 1.0
H2' A:DT8 4.6 0.0 1.0
H4' A:DT8 4.6 0.0 1.0
C2' A:DT8 4.7 0.0 1.0
H5' A:DT8 4.9 0.0 1.0

Sodium binding site 4 out of 8 in 6m6k

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Sodium binding site 4 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg Repeats within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na104

b:0.0
occ:1.00
OP2 A:3DR5 2.2 0.0 1.0
OP2 A:DG4 2.2 0.0 1.0
H5' A:DG4 2.5 0.0 1.0
H5'' A:DG4 2.6 0.0 1.0
C5' A:DG4 3.0 0.0 1.0
P A:DG4 3.5 0.0 1.0
O5' A:DG4 3.7 0.0 1.0
P A:3DR5 3.7 0.0 1.0
H3' A:DG4 4.0 0.0 1.0
C4' A:DG4 4.3 0.0 1.0
O5' A:3DR5 4.3 0.0 1.0
O3' A:DT3 4.4 0.0 1.0
C3' A:DG4 4.4 0.0 1.0
O3' A:DG4 4.4 0.0 1.0
OP1 A:DG4 4.7 0.0 1.0
H4' A:DG4 4.7 0.0 1.0
OP1 A:3DR5 4.8 0.0 1.0

Sodium binding site 5 out of 8 in 6m6k

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Sodium binding site 5 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg Repeats within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na105

b:0.0
occ:1.00
O2 A:DC6 2.4 0.0 1.0
N3 A:DC7 2.4 0.0 1.0
H22 A:DG9 2.4 0.0 1.0
H21 A:DG4 2.4 0.0 1.0
N3 A:DC2 2.5 0.0 1.0
N2 A:DG4 2.5 0.0 1.0
O2 A:DC2 2.5 0.0 1.0
N2 A:DG9 2.5 0.0 1.0
H21 A:DG9 2.8 0.0 1.0
C2 A:DC2 2.9 0.0 1.0
H41 A:DC7 2.9 0.0 1.0
C2 A:DG4 2.9 0.0 1.0
N3 A:DG4 2.9 0.0 1.0
C2 A:DC7 3.1 0.0 1.0
H22 A:DG4 3.1 0.0 1.0
O2 A:DC7 3.2 0.0 1.0
C4 A:DC7 3.2 0.0 1.0
N4 A:DC7 3.3 0.0 1.0
C2 A:DC6 3.4 0.0 1.0
H41 A:DC2 3.5 0.0 1.0
C2 A:DG9 3.5 0.0 1.0
C4 A:DC2 3.5 0.0 1.0
H1 A:DG9 3.8 0.0 1.0
N4 A:DC2 3.9 0.0 1.0
H1' A:DC6 3.9 0.0 1.0
N1 A:DG4 4.0 0.0 1.0
N3 A:DC6 4.0 0.0 1.0
N1 A:DG9 4.1 0.0 1.0
C4 A:DG4 4.1 0.0 1.0
N1 A:DC2 4.2 0.0 1.0
H1' A:DG4 4.2 0.0 1.0
N1 A:DC7 4.2 0.0 1.0
H42 A:DC7 4.2 0.0 1.0
H1 A:DG4 4.3 0.0 1.0
O2 A:DC1 4.3 0.0 1.0
N1 A:DC6 4.3 0.0 1.0
C5 A:DC7 4.4 0.0 1.0
N3 A:DG9 4.4 0.0 1.0
H5' A:DT3 4.4 0.0 1.0
H2'' A:DC7 4.5 0.0 1.0
C1' A:DC6 4.5 0.0 1.0
C6 A:DC7 4.7 0.0 1.0
C5 A:DC2 4.7 0.0 1.0
H2'' A:DC2 4.7 0.0 1.0
H1' A:DC2 4.8 0.0 1.0
H42 A:DC2 4.8 0.0 1.0
H5' A:DT8 4.9 0.0 1.0
O4' A:DC6 4.9 0.0 1.0
H2' A:DC7 4.9 0.0 1.0
C6 A:DC2 4.9 0.0 1.0
C6 A:DG4 5.0 0.0 1.0

Sodium binding site 6 out of 8 in 6m6k

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Sodium binding site 6 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg Repeats within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na106

b:0.0
occ:1.00
OP1 A:DC7 2.2 0.0 1.0
O4' A:DC7 2.4 0.0 1.0
H5' A:DC7 2.8 0.0 1.0
H6 A:DC7 2.8 0.0 1.0
C4' A:DC7 3.2 0.0 1.0
C5' A:DC7 3.3 0.0 1.0
H4' A:DC7 3.4 0.0 1.0
P A:DC7 3.5 0.0 1.0
C6 A:DC7 3.7 0.0 1.0
C1' A:DC7 3.7 0.0 1.0
O5' A:DC7 3.8 0.0 1.0
N1 A:DC7 4.1 0.0 1.0
H1' A:DC7 4.2 0.0 1.0
O3' A:DC6 4.3 0.0 1.0
H5'' A:DC7 4.3 0.0 1.0
C3' A:DC7 4.6 0.0 1.0
OP2 A:DC7 4.7 0.0 1.0
C2' A:DC7 4.7 0.0 1.0
C5 A:DC7 4.8 0.0 1.0
H2' A:DC7 4.8 0.0 1.0
H5 A:DC7 4.9 0.0 1.0

Sodium binding site 7 out of 8 in 6m6k

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Sodium binding site 7 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between 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 uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg Repeats within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na107

b:0.0
occ:1.00
OP1 A:DC2 2.3 0.0 1.0
OP2 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
O3' A:DC1 3.9 0.0 1.0
O5' A:DC2 3.9 0.0 1.0
H5'' A:DC2 4.0 0.0 1.0
C5' A:DC2 4.2 0.0 1.0
H3' A:DC1 4.3 0.0 1.0
C3' A:DC1 4.7 0.0 1.0

Sodium binding site 8 out of 8 in 6m6k

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Sodium binding site 8 out of 8 in the uc(Nmr) Solution Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg 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 Structure of A Dna Minidumbbell Containing An Abasic Bulge Between Two Cctg Repeats within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na108

b:0.0
occ:1.00
OP2 A:DC6 2.2 0.0 1.0
OP2 A:DC7 2.2 0.0 1.0
H3' A:DC6 2.4 0.0 1.0
C3' A:DC6 3.4 0.0 1.0
P A:DC7 3.6 0.0 1.0
P A:DC6 3.7 0.0 1.0
H5'' A:DC6 3.8 0.0 1.0
H2' A:DC6 3.8 0.0 1.0
O3' A:DC6 3.9 0.0 1.0
C2' A:DC6 4.1 0.0 1.0
H2'' A:DC6 4.2 0.0 1.0
O5' A:DC6 4.2 0.0 1.0
O5' A:DC7 4.3 0.0 1.0
C5' A:DC6 4.3 0.0 1.0
O3' A:3DR5 4.5 0.0 1.0
C4' A:DC6 4.5 0.0 1.0
OP1 A:DC6 4.7 0.0 1.0
OP1 A:DC7 4.8 0.0 1.0

Reference:

L.Wan, S.L.Lam, H.K.Lee, P.Guo. Rational Design of A Reversible MG2+/Edta-Controlled Molecular Switch Based on A Dna Minidumbbell. Chem.Commun.(Camb.) V. 56 10127 2020.
ISSN: ESSN 1364-548X
PubMed: 32870195
DOI: 10.1039/D0CC03774E
Page generated: Tue Dec 15 12:34:48 2020

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