Sodium in PDB 4gqd: Dna Holliday Junction Stabilized By Chlorine Halogen Bond.

The structure of Dna Holliday Junction Stabilized By Chlorine Halogen Bond., PDB code: 4gqd was solved by M.Carter, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.68 / 1.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.692, 23.565, 37.286, 90.00, 110.92, 90.00
R / Rfree (%)	26.4 / 30

The structure of Dna Holliday Junction Stabilized By Chlorine Halogen Bond. also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Dna Holliday Junction Stabilized By Chlorine Halogen Bond. (pdb code 4gqd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Holliday Junction Stabilized By Chlorine Halogen Bond., PDB code: 4gqd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Holliday Junction Stabilized By Chlorine Halogen Bond.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Holliday Junction Stabilized By Chlorine Halogen Bond. within 5.0Å range:

Sodium binding site 2 out of 3 in the Dna Holliday Junction Stabilized By Chlorine Halogen Bond.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Holliday Junction Stabilized By Chlorine Halogen Bond. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:28.1 occ:1.00 O B:HOH210 2.8 6.7 1.0 O D:HOH128 2.8 1.6 1.0 O2 D:DC32 3.1 10.9 0.4 O2 B:DC12 3.1 5.2 0.6 O B:HOH212 3.2 14.6 1.0 O4' D:DG33 3.3 12.0 0.4 O4' B:DG13 3.3 12.2 0.6 N3 B:DG13 3.6 1.6 0.6 N3 D:DG33 3.6 2.7 0.4 O4' D:DC32 3.6 14.0 0.4 C1' D:DG33 3.7 9.1 0.4 O4' B:DC12 3.8 11.6 0.6 C1' B:DG13 3.8 8.2 0.6 C4 B:DG13 4.0 1.6 0.6 C4 D:DG33 4.0 2.6 0.4 C1' D:DC32 4.0 13.6 0.4 N9 D:DG33 4.0 7.1 0.4 C1' B:DC12 4.0 10.8 0.6 N9 B:DG13 4.0 6.9 0.6 C2 D:DC32 4.2 11.9 0.4 C2 B:DG13 4.3 2.3 0.6 C2 B:DC12 4.3 7.1 0.6 C4' D:DC32 4.3 14.8 0.4 C4' B:DC12 4.3 13.1 0.6 C2 D:DG33 4.4 3.2 0.4 C4' D:DG33 4.4 13.0 0.4 C4' B:DG13 4.4 12.4 0.6 O3' B:DC12 4.5 14.3 0.6 O3' D:DC32 4.6 15.1 0.4 N2 B:DG13 4.6 4.1 0.6 N1 D:DC32 4.7 12.3 0.4 N2 D:DG33 4.7 4.2 0.4 O B:HOH223 4.7 18.9 1.0 N1 B:DC12 4.7 8.4 0.6 C5 B:DG13 5.0 1.9 0.6 C5 D:DG33 5.0 3.2 0.4 C3' B:DC12 5.0 13.7 0.6

Sodium binding site 3 out of 3 in the Dna Holliday Junction Stabilized By Chlorine Halogen Bond.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Holliday Junction Stabilized By Chlorine Halogen Bond. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:15.9 occ:1.00 O D:HOH123 2.1 12.7 1.0 OP1 B:DG19 2.6 21.2 0.6 OP1 D:DG39 2.7 22.6 0.4 O D:HOH102 3.2 21.4 1.0 P B:DG19 4.0 23.4 0.6 P D:DG39 4.1 23.5 0.4 O5' B:DC18 4.2 13.8 0.6 O5' D:DC38 4.3 18.4 0.4 OP1 B:DC18 4.6 16.0 0.6 O3' D:DC38 4.6 22.4 0.4 O3' B:DC18 4.7 20.1 0.6 C3' B:DC18 4.8 16.5 0.6 OP1 D:DC38 4.8 19.1 0.4 C4' D:DC38 4.9 19.3 0.4 C3' D:DC38 4.9 20.5 0.4 C4' B:DC18 4.9 14.3 0.6 O5' B:DG19 4.9 21.1 0.6 OP2 B:DG19 4.9 19.6 0.6 C5' D:DG39 4.9 21.5 0.4 O5' D:DG39 5.0 22.2 0.4 C5' B:DG19 5.0 20.3 0.6

M.Carter, A.R.Voth, M.R.Scholfield, B.Rummel, L.C.Sowers, P.S.Ho. Enthalpy-Entropy Compensation in Biomolecular Halogen Bonds Measured in Dna Junctions. Biochemistry V. 52 4891 2013.
ISSN: ISSN 0006-2960
PubMed: 23789744
DOI: 10.1021/BI400590H