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Sodium in PDB 6m0b: Solution uc(Nmr) Structures of Dna Minidumbbell Formed By 5'-Cttg Cgtg-3'.

Sodium Binding Sites:

The binding sites of Sodium atom in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed By 5'-Cttg Cgtg-3'. (pdb code 6m0b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed By 5'-Cttg Cgtg-3'., PDB code: 6m0b:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 6m0b

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Sodium binding site 1 out of 7 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed By 5'-Cttg Cgtg-3'.


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 By 5'-Cttg Cgtg-3'. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na101

b:0.0
occ:1.00
OP2 A:DG4 2.5 0.0 1.0
O3' A:DT3 2.7 0.0 1.0
H5'' A:DG4 2.8 0.0 1.0
P A:DG4 3.1 0.0 1.0
H1' A:DT3 3.5 0.0 1.0
C5' A:DG4 3.7 0.0 1.0
O5' A:DG4 3.8 0.0 1.0
H2'' A:DT3 3.8 0.0 1.0
H8 A:DG4 3.9 0.0 1.0
C3' A:DT3 3.9 0.0 1.0
O4' A:DG4 4.0 0.0 1.0
H2' A:DG4 4.0 0.0 1.0
C2' A:DT3 4.2 0.0 1.0
C8 A:DG4 4.3 0.0 1.0
C1' A:DT3 4.3 0.0 1.0
C4' A:DG4 4.4 0.0 1.0
H5' A:DG4 4.4 0.0 1.0
OP1 A:DG4 4.5 0.0 1.0
H4' A:DT3 4.5 0.0 1.0
N9 A:DG4 4.6 0.0 1.0
C4' A:DT3 4.6 0.0 1.0
H3' A:DT3 4.7 0.0 1.0
O4' A:DT3 4.7 0.0 1.0
C1' A:DG4 4.7 0.0 1.0
C2' A:DG4 4.8 0.0 1.0
H3' A:DG4 4.9 0.0 1.0
N7 A:DG4 5.0 0.0 1.0

Sodium binding site 2 out of 7 in 6m0b

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Sodium binding site 2 out of 7 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed By 5'-Cttg Cgtg-3'.


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 By 5'-Cttg Cgtg-3'. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na102

b:0.0
occ:1.00
OP2 A:DT7 2.5 0.0 1.0
O5' A:DG6 2.6 0.0 1.0
OP2 A:DG6 2.7 0.0 1.0
H3' A:DG6 2.9 0.0 1.0
P A:DG6 3.3 0.0 1.0
H2'' A:DC5 3.4 0.0 1.0
H72 A:DT7 3.4 0.0 1.0
H73 A:DT7 3.6 0.0 1.0
H4' A:DG6 3.7 0.0 1.0
C3' A:DG6 3.7 0.0 1.0
C5' A:DG6 3.8 0.0 1.0
H2' A:DC5 3.9 0.0 1.0
P A:DT7 3.9 0.0 1.0
C4' A:DG6 3.9 0.0 1.0
C7 A:DT7 4.0 0.0 1.0
C2' A:DC5 4.0 0.0 1.0
O3' A:DG6 4.2 0.0 1.0
O3' A:DC5 4.3 0.0 1.0
H3' A:DC5 4.4 0.0 1.0
OP1 A:DG6 4.4 0.0 1.0
H5' A:DG6 4.4 0.0 1.0
C3' A:DC5 4.4 0.0 1.0
H5'' A:DG6 4.5 0.0 1.0
H71 A:DT7 4.6 0.0 1.0
O5' A:DT7 4.8 0.0 1.0
H6 A:DT7 4.9 0.0 1.0
OP1 A:DT7 4.9 0.0 1.0

Sodium binding site 3 out of 7 in 6m0b

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Sodium binding site 3 out of 7 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed By 5'-Cttg Cgtg-3'.


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 By 5'-Cttg Cgtg-3'. 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 4.0 0.0 1.0
H5'' A:DT2 4.0 0.0 1.0
O5' A:DT2 4.2 0.0 1.0
O3' A:DC1 4.2 0.0 1.0
C5' A:DT2 4.3 0.0 1.0
H3' A:DC1 4.7 0.0 1.0

Sodium binding site 4 out of 7 in 6m0b

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Sodium binding site 4 out of 7 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed By 5'-Cttg Cgtg-3'.


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 By 5'-Cttg Cgtg-3'. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na104

b:0.0
occ:1.00
OP1 A:DG8 2.5 0.0 1.0
OP1 A:DT7 2.5 0.0 1.0
H5'' A:DT7 2.6 0.0 1.0
H3' A:DT7 2.9 0.0 1.0
C5' A:DT7 3.5 0.0 1.0
P A:DT7 3.7 0.0 1.0
C3' A:DT7 3.8 0.0 1.0
O5' A:DT7 3.8 0.0 1.0
P A:DG8 3.9 0.0 1.0
C4' A:DT7 4.1 0.0 1.0
H4' A:DT7 4.3 0.0 1.0
O3' A:DT7 4.3 0.0 1.0
H5' A:DT7 4.3 0.0 1.0
O3' A:DG6 4.5 0.0 1.0
O5' A:DG8 4.6 0.0 1.0
H2' A:DT7 4.9 0.0 1.0
OP2 A:DT7 4.9 0.0 1.0
OP2 A:DG8 5.0 0.0 1.0

Sodium binding site 5 out of 7 in 6m0b

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Sodium binding site 5 out of 7 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed By 5'-Cttg Cgtg-3'.


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 By 5'-Cttg Cgtg-3'. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na105

b:0.0
occ:1.00
OP1 A:DC5 2.6 0.0 1.0
O3' A:DC5 2.6 0.0 1.0
OP1 A:DG6 2.8 0.0 1.0
H4' A:DC5 3.0 0.0 1.0
H5' A:DC5 3.0 0.0 1.0
P A:DG6 3.3 0.0 1.0
C4' A:DC5 3.5 0.0 1.0
C3' A:DC5 3.6 0.0 1.0
C5' A:DC5 3.7 0.0 1.0
H3' A:DC5 3.9 0.0 1.0
P A:DC5 3.9 0.0 1.0
O5' A:DC5 4.3 0.0 1.0
OP2 A:DG6 4.3 0.0 1.0
H5'' A:DG6 4.4 0.0 1.0
H5' A:DG6 4.4 0.0 1.0
O5' A:DG6 4.5 0.0 1.0
C5' A:DG6 4.6 0.0 1.0
H5'' A:DC5 4.6 0.0 1.0
O3' A:DG4 4.7 0.0 1.0
O4' A:DC5 4.9 0.0 1.0
C2' A:DC5 4.9 0.0 1.0

Sodium binding site 6 out of 7 in 6m0b

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Sodium binding site 6 out of 7 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed By 5'-Cttg Cgtg-3'.


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 By 5'-Cttg Cgtg-3'. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na106

b:0.0
occ:1.00
OP1 A:DG4 2.5 0.0 1.0
OP2 A:DT3 2.6 0.0 1.0
O5' A:DT3 2.7 0.0 1.0
H3' A:DT3 2.8 0.0 1.0
P A:DT3 3.2 0.0 1.0
C3' A:DT3 3.8 0.0 1.0
P A:DG4 3.8 0.0 1.0
C5' A:DT3 3.9 0.0 1.0
OP1 A:DT3 4.2 0.0 1.0
C4' A:DT3 4.2 0.0 1.0
O5' A:DG4 4.2 0.0 1.0
O3' A:DT3 4.3 0.0 1.0
H4' A:DT3 4.3 0.0 1.0
O3' A:DT2 4.4 0.0 1.0
H5' A:DT3 4.5 0.0 1.0
H5'' A:DT3 4.6 0.0 1.0
H2' A:DT3 4.9 0.0 1.0
C2' A:DT3 5.0 0.0 1.0

Sodium binding site 7 out of 7 in 6m0b

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Sodium binding site 7 out of 7 in the Solution uc(Nmr) Structures of Dna Minidumbbell Formed By 5'-Cttg Cgtg-3'.


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 By 5'-Cttg Cgtg-3'. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na107

b:0.0
occ:1.00
OP1 A:DT3 2.5 0.0 1.0
O6 A:DG6 2.6 0.0 1.0
N7 A:DG6 2.7 0.0 1.0
H1' A:DT2 2.8 0.0 1.0
H5'' A:DT3 3.1 0.0 1.0
C6 A:DG6 3.1 0.0 1.0
C5 A:DG6 3.2 0.0 1.0
O2 A:DT2 3.4 0.0 1.0
P A:DT3 3.7 0.0 1.0
O5' A:DT3 3.7 0.0 1.0
C1' A:DT2 3.9 0.0 1.0
C5' A:DT3 3.9 0.0 1.0
C8 A:DG6 3.9 0.0 1.0
C2 A:DT2 4.3 0.0 1.0
O4' A:DT2 4.3 0.0 1.0
H4' A:DT3 4.3 0.0 1.0
H8 A:DG6 4.4 0.0 1.0
N1 A:DG6 4.4 0.0 1.0
C4 A:DG6 4.4 0.0 1.0
N1 A:DT2 4.5 0.0 1.0
H2'' A:DT2 4.6 0.0 1.0
H5' A:DT3 4.7 0.0 1.0
OP2 A:DT3 4.7 0.0 1.0
C4' A:DT3 4.7 0.0 1.0
H4' A:DG4 4.7 0.0 1.0
C2' A:DT2 4.8 0.0 1.0
N9 A:DG6 4.8 0.0 1.0
H1 A:DG6 4.8 0.0 1.0
O3' A:DT2 4.8 0.0 1.0
H22 A:DG4 5.0 0.0 1.0
H4' A:DT2 5.0 0.0 1.0

Reference:

C.K.Ngai, S.L.Lam, H.K.Lee, P.Guo. High-Resolution Structures of Dna Minidumbbells Comprising Type II Tetraloops with A Purine Minor Groove Residue. J.Phys.Chem.B 2020.
ISSN: ISSN 1089-5647
PubMed: 32484672
DOI: 10.1021/ACS.JPCB.0C03163
Page generated: Tue Dec 15 12:34:30 2020

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