Sodium in PDB 6a85: Crystal Structure of A Novel Dna Quadruplex

The structure of Crystal Structure of A Novel Dna Quadruplex, PDB code: 6a85 was solved by H.H.Liu, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.50 / 1.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	37.822, 46.651, 51.311, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 16.9

The structure of Crystal Structure of A Novel Dna Quadruplex also contains other interesting chemical elements:

Lead

(Pb)

1 atom

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of A Novel Dna Quadruplex (pdb code 6a85). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Crystal Structure of A Novel Dna Quadruplex, PDB code: 6a85:
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 Crystal Structure of A Novel Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Novel Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:26.5 occ:0.50 O6 A:DG2 2.8 16.9 1.0 O6 B:DG2 2.9 15.5 1.0 O A:HOH210 2.9 19.0 1.0 C6 B:DG2 3.6 14.1 1.0 NA B:NA101 3.6 21.9 0.5 C6 A:DG2 3.8 17.6 1.0 N1 B:DG2 3.8 14.6 1.0 N B:NH4102 3.9 22.2 0.5 N1 A:DG2 4.0 17.2 1.0 N7 A:DA1 4.6 19.2 1.0 C5 B:DG2 4.8 14.3 1.0 C8 A:DA1 4.9 19.5 1.0

Sodium binding site 2 out of 11 in the Crystal Structure of A Novel Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Novel Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:22.8 occ:0.50 NA A:NA105 2.8 24.6 0.5 O6 A:DG4 3.0 15.5 1.0 O6 B:DG4 3.1 15.7 1.0 N1 B:DA5 3.4 13.0 1.0 N1 A:DA5 3.4 13.3 1.0 C2 B:DA5 3.4 12.8 1.0 C2 A:DA5 3.4 14.4 1.0 NA A:NA113 3.7 25.4 0.5 C6 A:DG4 3.8 15.7 1.0 C6 B:DG4 3.8 12.1 1.0 N1 B:DG4 4.0 14.0 1.0 N1 A:DG4 4.1 15.7 1.0 N3 B:DA5 4.6 13.6 1.0 N3 A:DA5 4.6 12.8 1.0 C6 A:DA5 4.7 14.9 1.0 C6 B:DA5 4.7 13.4 1.0 C5 A:DG4 5.0 14.5 1.0

Sodium binding site 3 out of 11 in the Crystal Structure of A Novel Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Novel Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:24.6 occ:0.50 NA A:NA104 2.8 22.8 0.5 O6 B:DG6 3.0 13.0 1.0 O6 A:DG6 3.0 14.0 1.0 N1 A:DA5 3.4 13.3 1.0 C2 A:DA5 3.4 14.4 1.0 C2 B:DA5 3.4 12.8 1.0 N1 B:DA5 3.5 13.0 1.0 NA A:NA106 3.7 25.7 0.5 C6 B:DG6 3.9 12.7 1.0 C6 A:DG6 3.9 13.5 1.0 N1 B:DG6 4.1 11.4 1.0 N1 A:DG6 4.2 12.7 1.0 N3 A:DA5 4.5 12.8 1.0 N3 B:DA5 4.5 13.6 1.0 C6 A:DA5 4.6 14.9 1.0 C6 B:DA5 4.6 13.4 1.0

Sodium binding site 4 out of 11 in the Crystal Structure of A Novel Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of A Novel Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:25.7 occ:0.50 O6 A:DG6 2.9 14.0 1.0 O6 B:DG6 3.0 13.0 1.0 O4 B:DT8 3.1 12.2 1.0 O4 A:DT8 3.1 12.2 1.0 NA A:NA107 3.4 19.2 0.5 NA A:NA105 3.7 24.6 0.5 C6 B:DG6 3.7 12.7 1.0 C6 A:DG6 3.7 13.5 1.0 N1 B:DG6 4.0 11.4 1.0 C4 B:DT8 4.0 10.2 1.0 N1 A:DG6 4.0 12.7 1.0 C4 A:DT8 4.0 10.9 1.0 N3 B:DT8 4.3 11.2 1.0 N3 A:DT8 4.4 10.1 1.0 C5 B:DG6 4.8 12.4 1.0 C5 A:DG6 4.9 14.2 1.0

Sodium binding site 5 out of 11 in the Crystal Structure of A Novel Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of A Novel Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:19.2 occ:0.50 O6 B:DG9 2.8 9.1 1.0 O6 A:DG9 2.9 9.7 1.0 O4 B:DT8 2.9 12.2 1.0 O4 A:DT8 2.9 12.2 1.0 NA A:NA108 3.4 19.9 0.5 NA A:NA106 3.4 25.7 0.5 C6 B:DG9 3.8 8.2 1.0 C6 A:DG9 3.8 8.3 1.0 C4 B:DT8 3.8 10.2 1.0 C4 A:DT8 3.8 10.9 1.0 N1 B:DG9 4.1 8.0 1.0 N1 A:DG9 4.1 8.3 1.0 N3 B:DT8 4.1 11.2 1.0 N3 A:DT8 4.2 10.1 1.0

Sodium binding site 6 out of 11 in the Crystal Structure of A Novel Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of A Novel Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na108 b:19.9 occ:0.50 O6 A:DG10 2.9 9.2 1.0 O6 B:DG10 2.9 9.0 1.0 O6 B:DG9 2.9 9.1 1.0 O6 A:DG9 2.9 9.7 1.0 NA A:NA107 3.4 19.2 0.5 NA A:NA109 3.5 21.5 0.5 C6 B:DG9 3.7 8.2 1.0 C6 A:DG9 3.7 8.3 1.0 C6 A:DG10 3.8 9.4 1.0 C6 B:DG10 3.8 8.9 1.0 N1 B:DG9 3.9 8.0 1.0 N1 A:DG9 4.0 8.3 1.0 N1 B:DG10 4.1 9.8 1.0 N1 A:DG10 4.1 9.5 1.0 C5 B:DG9 4.8 9.7 1.0 C5 A:DG9 4.9 8.8 1.0

Sodium binding site 7 out of 11 in the Crystal Structure of A Novel Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of A Novel Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:21.5 occ:0.50 O6 A:DG11 2.9 11.5 1.0 O6 B:DG11 2.9 11.0 1.0 O6 B:DG10 2.9 9.0 1.0 O6 A:DG10 2.9 9.2 1.0 NA A:NA108 3.5 19.9 0.5 C6 B:DG10 3.7 8.9 1.0 C6 A:DG10 3.7 9.4 1.0 C6 A:DG11 3.8 10.3 1.0 C6 B:DG11 3.8 9.5 1.0 NA A:NA110 3.8 26.7 0.5 N1 B:DG10 4.0 9.8 1.0 N1 A:DG10 4.0 9.5 1.0 N1 A:DG11 4.0 8.2 1.0 N1 B:DG11 4.0 9.1 1.0 C5 B:DG10 4.9 9.6 1.0 C5 A:DG10 4.9 8.5 1.0

Sodium binding site 8 out of 11 in the Crystal Structure of A Novel Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of A Novel Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na110 b:26.7 occ:0.50 LI A:LI101 2.8 13.4 0.5 O4 B:DT12 3.1 19.1 1.0 O4 A:DT12 3.1 17.2 1.0 O6 A:DG11 3.1 11.5 1.0 O6 B:DG11 3.2 11.0 1.0 NA A:NA109 3.8 21.5 0.5 C6 A:DG11 3.9 10.3 1.0 C6 B:DG11 3.9 9.5 1.0 C4 B:DT12 4.0 14.5 1.0 C4 A:DT12 4.0 13.3 1.0 N1 A:DG11 4.1 8.2 1.0 N1 B:DG11 4.1 9.1 1.0 N3 B:DT12 4.2 14.6 1.0 N3 A:DT12 4.3 13.1 1.0

Sodium binding site 9 out of 11 in the Crystal Structure of A Novel Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of A Novel Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na111 b:17.1 occ:0.50 O6 B:DG15 2.9 11.7 1.0 O A:HOH263 2.9 10.2 1.0 O6 A:DG15 3.0 11.7 1.0 O B:HOH216 3.2 10.7 1.0 LI A:LI102 3.3 20.5 0.5 C6 B:DG15 3.6 11.3 1.0 C6 A:DG15 3.8 9.5 1.0 PB A:PB112 3.8 13.6 0.5 N1 B:DG15 3.8 10.3 1.0 N1 A:DG15 4.1 9.4 1.0 O2 B:DC14 4.6 12.8 1.0 N3 B:DC14 4.6 9.5 1.0 N3 A:DC14 4.8 10.3 1.0 O2 A:DC14 4.8 11.2 1.0 C5 B:DG15 4.9 10.3 1.0

Sodium binding site 10 out of 11 in the Crystal Structure of A Novel Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of A Novel Dna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na113 b:25.4 occ:0.50 NA B:NA101 2.8 21.9 0.5 O6 B:DG4 2.9 15.7 1.0 O6 A:DG4 3.0 15.5 1.0 N1 B:DA3 3.4 12.9 1.0 C2 B:DA3 3.5 15.7 1.0 C2 A:DA3 3.5 15.7 1.0 N1 A:DA3 3.6 15.1 1.0 NA A:NA104 3.7 22.8 0.5 C6 B:DG4 3.8 12.1 1.0 C6 A:DG4 3.8 15.7 1.0 N1 B:DG4 4.0 14.0 1.0 N1 A:DG4 4.1 15.7 1.0 N3 A:DA3 4.6 16.4 1.0 N3 B:DA3 4.6 15.6 1.0 C6 B:DA3 4.6 13.7 1.0 C6 A:DA3 4.7 15.9 1.0

H.H.Liu, R.Wang, X.Yu, F.S.Shen, W.X.Lan, P.Haruehanroengra, Q.Q.Yao, J.Zhang, Y.Q.Chen, S.H.Li, B.X.Wu, L.N.Zheng, J.B.Ma, J.Z.Lin, C.Y.Cao, J.X.Li, J.Sheng, J.H.Gan. High-Resolution Dna Quadruplex Structure Containing All the A-, G-, C-, T-Tetrads. Nucleic Acids Res. V. 46 11627 2018.
ISSN: ESSN 1362-4962
PubMed: 30285239
DOI: 10.1093/NAR/GKY902