Sodium in PDB 7vck: uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg Repeats

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>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg Repeats (pdb code 7vck). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg Repeats, PDB code: 7vck:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg 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 Structures of A Hairpin Formed By Ggcctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:0.0 occ:1.00 OP1 A:DT5 2.2 0.0 1.0 OP1 A:DG6 2.2 0.0 1.0 H4' A:DT5 2.6 0.0 1.0 P A:DG6 3.2 0.0 1.0 O3' A:DT5 3.2 0.0 1.0 C4' A:DT5 3.5 0.0 1.0 H5' A:DT5 3.6 0.0 1.0 P A:DT5 3.6 0.0 1.0 C3' A:DT5 3.8 0.0 1.0 OP2 A:DG6 3.9 0.0 1.0 C5' A:DT5 4.0 0.0 1.0 H3' A:DT5 4.0 0.0 1.0 O5' A:DT5 4.3 0.0 1.0 H5'' A:DG6 4.3 0.0 1.0 O3' A:DC4 4.4 0.0 1.0 O5' A:DG6 4.5 0.0 1.0 O4' A:DT5 4.6 0.0 1.0 OP2 A:DT5 4.7 0.0 1.0 C5' A:DG6 4.9 0.0 1.0

Sodium binding site 2 out of 11 in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg 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 Structures of A Hairpin Formed By Ggcctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.0 occ:1.00 OP2 A:DC9 2.2 0.0 1.0 O6 A:DG12 2.2 0.0 1.0 O4 A:DT11 2.3 0.0 1.0 C4 A:DT11 3.2 0.0 1.0 C6 A:DG12 3.3 0.0 1.0 H72 A:DT11 3.4 0.0 1.0 H1 A:DG12 3.5 0.0 1.0 P A:DC9 3.6 0.0 1.0 H73 A:DT11 3.6 0.0 1.0 N1 A:DG12 3.8 0.0 1.0 C7 A:DT11 3.8 0.0 1.0 H5 A:DC9 3.9 0.0 1.0 C5 A:DT11 4.0 0.0 1.0 H3' A:DG8 4.1 0.0 1.0 N3 A:DT11 4.2 0.0 1.0 OP1 A:DC9 4.2 0.0 1.0 H3 A:DT11 4.3 0.0 1.0 O5' A:DC9 4.3 0.0 1.0 H6 A:DC9 4.5 0.0 1.0 C5 A:DG12 4.5 0.0 1.0 O3' A:DG8 4.6 0.0 1.0 C5 A:DC9 4.7 0.0 1.0 C3' A:DG8 4.8 0.0 1.0 H71 A:DT11 4.9 0.0 1.0

Sodium binding site 3 out of 11 in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg 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 Structures of A Hairpin Formed By Ggcctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.0 occ:1.00 OP1 A:DC10 2.3 0.0 1.0 OP2 A:DC10 2.3 0.0 1.0 N3 A:DG12 2.4 0.0 1.0 H2'' A:DG12 2.6 0.0 1.0 P A:DC10 2.7 0.0 1.0 C2 A:DG12 2.9 0.0 1.0 H22 A:DG12 2.9 0.0 1.0 N2 A:DG12 3.0 0.0 1.0 C4 A:DG12 3.2 0.0 1.0 C2' A:DG12 3.5 0.0 1.0 O3' A:DC9 3.6 0.0 1.0 H1' A:DG12 3.8 0.0 1.0 H21 A:DG12 3.8 0.0 1.0 N9 A:DG12 3.8 0.0 1.0 C1' A:DG12 3.9 0.0 1.0 H2' A:DG12 4.0 0.0 1.0 N1 A:DG12 4.0 0.0 1.0 O5' A:DC10 4.0 0.0 1.0 C5 A:DG12 4.3 0.0 1.0 H5'' A:DC9 4.4 0.0 1.0 H1 A:DG12 4.5 0.0 1.0 H3' A:DC9 4.6 0.0 1.0 H72 A:DT11 4.6 0.0 1.0 C6 A:DG12 4.6 0.0 1.0 O3' A:DG12 4.7 0.0 1.0 C3' A:DC9 4.7 0.0 1.0 C3' A:DG12 4.7 0.0 1.0 HO3' A:DG12 4.8 0.0 1.0 H5'' A:DC10 4.8 0.0 1.0 H71 A:DT11 4.9 0.0 1.0

Sodium binding site 4 out of 11 in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg 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 Structures of A Hairpin Formed By Ggcctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.0 occ:1.00 OP2 A:DC4 2.2 0.0 1.0 OP1 A:DC3 2.3 0.0 1.0 H5'' A:DC3 2.5 0.0 1.0 O5' A:DC3 2.6 0.0 1.0 P A:DC3 3.0 0.0 1.0 H5 A:DC4 3.0 0.0 1.0 C5' A:DC3 3.0 0.0 1.0 H3' A:DC3 3.0 0.0 1.0 P A:DC4 3.3 0.0 1.0 O3' A:DC3 3.6 0.0 1.0 C3' A:DC3 3.6 0.0 1.0 OP2 A:DC3 3.7 0.0 1.0 C5 A:DC4 3.8 0.0 1.0 C4' A:DC3 3.9 0.0 1.0 H6 A:DC4 3.9 0.0 1.0 H5' A:DC3 3.9 0.0 1.0 OP1 A:DC4 4.1 0.0 1.0 C6 A:DC4 4.3 0.0 1.0 O3' A:DG2 4.4 0.0 1.0 H4' A:DC3 4.4 0.0 1.0 H42 A:DC4 4.5 0.0 1.0 H5'' A:DC4 4.6 0.0 1.0 O5' A:DC4 4.7 0.0 1.0 C4 A:DC4 4.9 0.0 1.0 O4' A:DC3 5.0 0.0 1.0

Sodium binding site 5 out of 11 in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg 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 Structures of A Hairpin Formed By Ggcctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:0.0 occ:1.00 H3' A:DG7 2.2 0.0 1.0 OP2 A:DG8 2.2 0.0 1.0 OP2 A:DG7 2.2 0.0 1.0 O3' A:DG6 2.5 0.0 1.0 P A:DG7 3.0 0.0 1.0 H2'' A:DG6 3.1 0.0 1.0 C3' A:DG7 3.2 0.0 1.0 P A:DG8 3.4 0.0 1.0 C3' A:DG6 3.6 0.0 1.0 O3' A:DG7 3.6 0.0 1.0 H5'' A:DG7 3.7 0.0 1.0 H3' A:DG6 3.8 0.0 1.0 C2' A:DG6 3.9 0.0 1.0 O5' A:DG7 3.9 0.0 1.0 H2' A:DG7 4.0 0.0 1.0 C2' A:DG7 4.0 0.0 1.0 C5' A:DG7 4.1 0.0 1.0 H2'' A:DG7 4.2 0.0 1.0 C4' A:DG7 4.2 0.0 1.0 OP1 A:DG7 4.2 0.0 1.0 OP1 A:DG8 4.2 0.0 1.0 H2' A:DG6 4.5 0.0 1.0 O5' A:DG8 4.6 0.0 1.0 H4' A:DG7 4.7 0.0 1.0 H1' A:DG6 4.7 0.0 1.0 C1' A:DG6 4.9 0.0 1.0 C4' A:DG6 4.9 0.0 1.0

Sodium binding site 6 out of 11 in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg 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 Structures of A Hairpin Formed By Ggcctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:0.0 occ:1.00 O2 A:DC4 2.2 0.0 1.0 O2 A:DT5 2.3 0.0 1.0 O6 A:DG6 2.4 0.0 1.0 N7 A:DG6 2.4 0.0 1.0 N4 A:DC3 2.5 0.0 1.0 C4 A:DC3 2.8 0.0 1.0 H1' A:DT5 2.9 0.0 1.0 C5 A:DG6 2.9 0.0 1.0 C6 A:DG6 2.9 0.0 1.0 H42 A:DC3 2.9 0.0 1.0 C2 A:DT5 3.0 0.0 1.0 H41 A:DC3 3.0 0.0 1.0 C5 A:DC3 3.1 0.0 1.0 H5 A:DC3 3.3 0.0 1.0 C2 A:DC4 3.4 0.0 1.0 N3 A:DC3 3.4 0.0 1.0 N1 A:DT5 3.6 0.0 1.0 C8 A:DG6 3.6 0.0 1.0 C1' A:DT5 3.7 0.0 1.0 N3 A:DT5 3.7 0.0 1.0 H3 A:DT5 3.8 0.0 1.0 H1' A:DC4 3.8 0.0 1.0 C6 A:DC3 3.9 0.0 1.0 N3 A:DC4 3.9 0.0 1.0 H8 A:DG6 4.1 0.0 1.0 C2 A:DC3 4.1 0.0 1.0 O6 A:DG8 4.2 0.0 1.0 C4 A:DG6 4.2 0.0 1.0 N1 A:DG6 4.3 0.0 1.0 O4' A:DT5 4.3 0.0 1.0 H1 A:DG8 4.3 0.0 1.0 N1 A:DC3 4.4 0.0 1.0 N1 A:DC4 4.4 0.0 1.0 C6 A:DT5 4.5 0.0 1.0 C1' A:DC4 4.6 0.0 1.0 C4 A:DT5 4.6 0.0 1.0 N9 A:DG6 4.6 0.0 1.0 H6 A:DC3 4.6 0.0 1.0 H2' A:DC3 4.7 0.0 1.0 H1 A:DG6 4.7 0.0 1.0 C5 A:DT5 4.9 0.0 1.0 H2'' A:DT5 4.9 0.0 1.0 C2' A:DT5 4.9 0.0 1.0 N1 A:DG8 5.0 0.0 1.0 C6 A:DG8 5.0 0.0 1.0

Sodium binding site 7 out of 11 in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg 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 Structures of A Hairpin Formed By Ggcctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:0.0 occ:1.00 OP2 A:DG12 2.2 0.0 1.0 OP2 A:DT11 2.2 0.0 1.0 O5' A:DT11 2.5 0.0 1.0 H3' A:DT11 2.9 0.0 1.0 P A:DT11 3.0 0.0 1.0 H5'' A:DT11 3.0 0.0 1.0 C5' A:DT11 3.2 0.0 1.0 P A:DG12 3.6 0.0 1.0 C3' A:DT11 3.7 0.0 1.0 O3' A:DT11 4.0 0.0 1.0 O3' A:DC10 4.0 0.0 1.0 C4' A:DT11 4.0 0.0 1.0 OP1 A:DT11 4.1 0.0 1.0 H5' A:DT11 4.2 0.0 1.0 H3' A:DC10 4.3 0.0 1.0 O5' A:DG12 4.3 0.0 1.0 H4' A:DT11 4.5 0.0 1.0 C3' A:DC10 4.7 0.0 1.0 OP1 A:DG12 4.7 0.0 1.0 C2' A:DT11 5.0 0.0 1.0 H2' A:DT11 5.0 0.0 1.0

Sodium binding site 8 out of 11 in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg 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 Structures of A Hairpin Formed By Ggcctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:0.0 occ:1.00 OP2 A:DC3 2.3 0.0 1.0 OP1 A:DG2 2.3 0.0 1.0 H3' A:DG2 2.3 0.0 1.0 OP2 A:DG2 2.4 0.0 1.0 P A:DG2 2.7 0.0 1.0 H42 A:DC4 2.7 0.0 1.0 C3' A:DG2 3.4 0.0 1.0 N4 A:DC4 3.4 0.0 1.0 O5' A:DG2 3.5 0.0 1.0 P A:DC3 3.5 0.0 1.0 H41 A:DC4 3.6 0.0 1.0 H2' A:DG2 3.7 0.0 1.0 O3' A:DG2 3.8 0.0 1.0 C2' A:DG2 4.0 0.0 1.0 O3' A:DG1 4.2 0.0 1.0 H2'' A:DG2 4.3 0.0 1.0 C5' A:DG2 4.3 0.0 1.0 H5' A:DG2 4.4 0.0 1.0 C4' A:DG2 4.4 0.0 1.0 OP1 A:DC3 4.5 0.0 1.0 H5 A:DC4 4.5 0.0 1.0 C4 A:DC4 4.6 0.0 1.0 H3' A:DG1 4.6 0.0 1.0 O5' A:DC3 4.7 0.0 1.0 H4' A:DG2 4.9 0.0 1.0 H2'' A:DG1 4.9 0.0 1.0 C3' A:DG1 4.9 0.0 1.0

Sodium binding site 9 out of 11 in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:0.0 occ:1.00 OP1 A:DG7 2.2 0.0 1.0 O5' A:DG6 2.3 0.0 1.0 H4' A:DG6 2.8 0.0 1.0 OP2 A:DG6 3.0 0.0 1.0 P A:DG6 3.0 0.0 1.0 C5' A:DG6 3.3 0.0 1.0 C4' A:DG6 3.4 0.0 1.0 H3' A:DG6 3.4 0.0 1.0 OP1 A:DG6 3.5 0.0 1.0 P A:DG7 3.6 0.0 1.0 C3' A:DG6 3.8 0.0 1.0 H5' A:DG6 3.9 0.0 1.0 H5'' A:DG6 4.2 0.0 1.0 O3' A:DG6 4.2 0.0 1.0 O5' A:DG7 4.3 0.0 1.0 O3' A:DT5 4.5 0.0 1.0 O4' A:DG6 4.7 0.0 1.0 OP2 A:DG7 4.8 0.0 1.0

Sodium binding site 10 out of 11 in the uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg Repeats


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of uc(Nmr) Solution Structures of A Hairpin Formed By Ggcctg Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na110 b:0.0 occ:1.00 OP1 A:DT11 2.2 0.0 1.0 O2 A:DC10 2.3 0.0 1.0 H1' A:DC10 3.1 0.0 1.0 H21 A:DG1 3.1 0.0 1.0 H2'' A:DC10 3.2 0.0 1.0 C2 A:DC10 3.3 0.0 1.0 H5' A:DT11 3.5 0.0 1.0 P A:DT11 3.6 0.0 1.0 N2 A:DG1 3.7 0.0 1.0 C1' A:DC10 3.8 0.0 1.0 C2' A:DC10 4.0 0.0 1.0 H22 A:DG1 4.1 0.0 1.0 O3' A:DC10 4.1 0.0 1.0 N1 A:DC10 4.1 0.0 1.0 N3 A:DC10 4.1 0.0 1.0 H1 A:DG1 4.3 0.0 1.0 C5' A:DT11 4.4 0.0 1.0 O5' A:DT11 4.4 0.0 1.0 C2 A:DG1 4.6 0.0 1.0 C3' A:DC10 4.6 0.0 1.0 OP2 A:DT11 4.7 0.0 1.0 H5'' A:DT11 4.8 0.0 1.0 N1 A:DG1 4.8 0.0 1.0 H2' A:DC10 4.8 0.0 1.0

J.Yi, L.Wan, Y.Liu, S.L.Lam, H.Y.E.Chan, D.Han, P.Guo. uc(Nmr) Solution Structures of D(Ggcctg)N Repeats Associated with Spinocerebellar Ataxia Type 36. Int.J.Biol.Macromol. V. 201 607 2022.
ISSN: ISSN 0141-8130
DOI: 10.1016/J.IJBIOMAC.2022.01.097