Fluorine in PDB 4gsi: Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference.

The structure of Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference., PDB code: 4gsi was solved by P.S.Ho, M.Carter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.61 / 2.38
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.213, 23.917, 77.450, 90.00, 114.80, 90.00
R / Rfree (%)	22.5 / 29.1

The binding sites of Fluorine atom in the Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference. (pdb code 4gsi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference., PDB code: 4gsi:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference. within 5.0Å range: probe atom residue distance (Å) B Occ A:F7 b:0.1 occ:0.40 F5 A:UFP7 0.0 0.1 0.4 C5 E:DC207 1.0 0.1 0.6 C5 A:UFP7 1.3 0.1 0.4 C4 E:DC207 1.9 0.1 0.6 C6 E:DC207 2.1 1.6 0.6 C4 A:UFP7 2.3 0.1 0.4 C6 A:UFP7 2.3 1.6 0.4 N4 E:DC207 2.4 0.1 0.6 O5' A:DA6 2.6 15.3 0.4 O5' E:DA206 2.7 16.8 0.6 O4 A:UFP7 2.7 0.1 0.4 N3 E:DC207 3.1 0.1 0.6 OP1 E:DA206 3.2 16.6 0.6 P E:DA206 3.2 17.9 0.6 P A:DA6 3.2 16.7 0.4 OP1 A:DA6 3.2 15.3 0.4 N1 E:DC207 3.3 3.3 0.6 C5' A:DA6 3.5 14.1 0.4 OP2 E:DA206 3.5 21.1 0.6 C5' E:DA206 3.5 16.4 0.6 OP2 A:DA6 3.5 20.1 0.4 N3 A:UFP7 3.5 0.2 0.4 N1 A:UFP7 3.6 2.8 0.4 C2 E:DC207 3.6 2.5 0.6 N7 C:DA26 3.8 1.4 0.4 N7 G:DA226 3.8 1.6 0.6 O6 H:DG233 3.8 3.0 0.6 O6 D:DG33 3.8 3.1 0.4 C8 C:DA26 3.8 3.3 0.4 O E:HOH314 3.9 17.6 1.0 C8 G:DA226 3.9 3.3 0.6 N4 A:DC8 3.9 0.1 0.4 N4 E:DC208 3.9 0.1 0.6 C2 A:UFP7 4.1 2.4 0.4 C3' A:DA6 4.2 11.3 0.4 C3' E:DA206 4.2 15.0 0.6 C5 C:DA26 4.3 0.1 0.4 C5 G:DA226 4.3 0.1 0.6 C4' A:DA6 4.4 11.5 0.4 N9 C:DA26 4.4 4.5 0.4 C4' E:DA206 4.4 14.4 0.6 N9 G:DA226 4.4 4.5 0.6 C1' E:DC207 4.5 5.8 0.6 C2' A:DA6 4.6 9.2 0.4 O4' E:DC207 4.6 9.0 0.6 C4 C:DA26 4.7 1.6 0.4 C2' E:DA206 4.7 12.3 0.6 C4 G:DA226 4.7 1.6 0.6 O3' E:DT205 4.7 21.0 0.6 C6 H:DG233 4.7 0.1 0.6 O3' A:DT5 4.7 20.1 0.4 C6 D:DG33 4.8 0.1 0.4 O5' E:DC207 4.8 17.6 0.6 C1' A:UFP7 4.8 4.6 0.4 O4' A:UFP7 4.8 6.6 0.4 O5' A:UFP7 4.8 12.1 0.4 C2' C:DA26 4.9 7.9 0.4 O2 E:DC207 4.9 7.5 0.6 C2' G:DA226 4.9 7.6 0.6 C4 A:DC8 5.0 1.0 0.4 C4 E:DC208 5.0 1.1 0.6 C6 G:DA226 5.0 0.1 0.6 C6 C:DA26 5.0 0.1 0.4

Fluorine binding site 2 out of 4 in the Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference. within 5.0Å range: probe atom residue distance (Å) B Occ C:F27 b:12.7 occ:0.40 F5 C:UFP27 0.0 12.7 0.4 C5 G:DC227 1.0 0.6 0.6 C5 C:UFP27 1.3 9.8 0.4 C6 G:DC227 2.0 1.6 0.6 C4 G:DC227 2.2 0.1 0.6 C4 C:UFP27 2.3 9.2 0.4 C6 C:UFP27 2.3 10.4 0.4 O5' G:DA226 2.6 11.8 0.6 N4 G:DC227 2.7 0.1 0.6 O4 C:UFP27 2.7 7.8 0.4 O5' C:DA26 2.7 13.6 0.4 N1 G:DC227 3.2 0.8 0.6 OP2 G:DA226 3.3 12.3 0.6 P G:DA226 3.3 11.6 0.6 N3 G:DC227 3.4 1.6 0.6 P C:DA26 3.4 13.9 0.4 N3 C:UFP27 3.5 10.0 0.4 OP1 C:DA26 3.5 12.1 0.4 OP2 C:DA26 3.6 15.1 0.4 N1 C:UFP27 3.6 10.5 0.4 C8 E:DA206 3.6 4.5 0.6 N7 E:DA206 3.6 0.1 0.6 N7 A:DA6 3.6 0.1 0.4 C5' C:DA26 3.6 12.1 0.4 C8 A:DA6 3.6 3.7 0.4 C5' G:DA226 3.6 11.0 0.6 OP1 G:DA226 3.7 9.9 0.6 C2 G:DC227 3.8 1.7 0.6 O6 B:DG13 3.9 2.7 0.4 O6 F:DG213 4.0 2.7 0.6 C3' C:DA26 4.0 10.9 0.4 C3' G:DA226 4.0 10.4 0.6 O B:HOH108 4.0 1.2 1.0 C2 C:UFP27 4.1 10.8 0.4 C5 A:DA6 4.1 0.7 0.4 C5 E:DA206 4.1 1.0 0.6 N9 E:DA206 4.1 5.7 0.6 N9 A:DA6 4.1 4.4 0.4 C4' C:DA26 4.4 10.1 0.4 C4' G:DA226 4.4 9.4 0.6 C4 E:DA206 4.4 2.8 0.6 C4 A:DA6 4.4 2.2 0.4 C1' G:DC227 4.5 5.1 0.6 O4' G:DC227 4.5 9.1 0.6 N4 G:DC228 4.5 21.9 0.6 N4 C:DC28 4.5 21.8 0.4 C2' C:DA26 4.6 7.9 0.4 C2' G:DA226 4.6 7.6 0.6 C2' E:DA206 4.6 12.3 0.6 O1P C:UFP27 4.6 11.6 0.4 C2' A:DA6 4.6 9.2 0.4 O5' G:DC227 4.6 11.2 0.6 O5' C:UFP27 4.7 13.1 0.4 OP2 G:DC227 4.8 10.2 0.6 O3' G:DT225 4.8 12.2 0.6 C1' C:UFP27 4.8 12.2 0.4 O4' C:UFP27 4.8 14.6 0.4 C6 B:DG13 4.9 0.1 0.4 C6 F:DG213 4.9 0.1 0.6 C1' E:DA206 4.9 10.9 0.6 C6 A:DA6 4.9 0.1 0.4 C6 E:DA206 4.9 0.1 0.6 O3' C:DT25 4.9 15.7 0.4 C1' A:DA6 4.9 8.8 0.4 O3' C:DA26 5.0 11.6 0.4

Fluorine binding site 3 out of 4 in the Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference. within 5.0Å range: probe atom residue distance (Å) B Occ F:F217 b:31.8 occ:0.60 F5 F:UFP217 0.0 31.8 0.6 C5 F:UFP217 1.3 30.1 0.6 C5 B:DC17 2.2 22.9 0.4 C4 F:UFP217 2.3 29.8 0.6 C6 F:UFP217 2.3 30.5 0.6 N4 F:DC218 2.7 37.4 0.6 N4 B:DC18 2.7 37.3 0.4 C6 B:DC17 2.7 24.4 0.4 O4 F:UFP217 2.7 28.6 0.6 C4 B:DC17 3.4 22.3 0.4 C4 F:DC218 3.4 36.5 0.6 C4 B:DC18 3.4 36.4 0.4 N3 F:UFP217 3.5 28.4 0.6 N1 F:UFP217 3.6 29.0 0.6 N4 B:DC17 3.8 20.2 0.4 C5 F:DC218 4.0 36.3 0.6 C5 B:DC18 4.0 36.2 0.4 N1 B:DC17 4.1 24.4 0.4 C2 F:UFP217 4.1 28.1 0.6 N3 F:DC218 4.2 35.9 0.6 N3 B:DC18 4.2 35.8 0.4 O F:HOH313 4.4 9.3 1.0 O6 E:DG203 4.5 25.7 0.6 O6 A:DG3 4.5 25.7 0.4 N3 B:DC17 4.5 22.8 0.4 C2' B:DA16 4.6 15.9 0.4 C2' F:DA216 4.6 16.4 0.6 C8 F:DA216 4.7 7.2 0.6 C8 B:DA16 4.7 7.1 0.4 C1' F:UFP217 4.8 27.7 0.6 C2 B:DC17 4.8 24.0 0.4 N9 B:DA16 4.9 8.7 0.4 N9 F:DA216 4.9 8.8 0.6 OP2 B:DC17 4.9 24.1 0.4 C2' B:DC17 5.0 25.6 0.4 C2' F:UFP217 5.0 27.4 0.6

Fluorine binding site 4 out of 4 in the Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Dna Holliday Junction Stabilized By Fluorine Halogen Bond. F2J Construct of Related Reference. within 5.0Å range: probe atom residue distance (Å) B Occ H:F237 b:7.5 occ:0.60 F5 H:UFP237 0.0 7.5 0.6 C5 H:UFP237 1.3 5.4 0.6 C5 D:DC37 1.8 7.7 0.4 C4 H:UFP237 2.3 2.1 0.6 C6 H:UFP237 2.3 9.3 0.6 C6 D:DC37 2.6 10.8 0.4 N4 H:DC238 2.7 21.4 0.6 N4 D:DC38 2.7 21.5 0.4 C4 D:DC37 2.7 6.3 0.4 O4 H:UFP237 2.7 0.1 0.6 N4 D:DC37 3.0 3.8 0.4 C4 D:DC38 3.4 21.2 0.4 C4 H:DC238 3.4 21.1 0.6 N3 H:UFP237 3.5 2.5 0.6 N1 H:UFP237 3.6 7.6 0.6 N1 D:DC37 3.7 10.9 0.4 N3 D:DC37 3.8 7.8 0.4 N3 H:DC238 3.8 21.2 0.6 N3 D:DC38 3.8 21.3 0.4 O6 G:DG223 3.9 5.2 0.6 O6 C:DG23 3.9 5.9 0.4 C8 H:DA236 4.0 4.2 0.6 C8 D:DA36 4.0 3.8 0.4 C2 H:UFP237 4.1 5.7 0.6 N9 H:DA236 4.2 6.0 0.6 N9 D:DA36 4.2 5.3 0.4 C2 D:DC37 4.2 10.0 0.4 N7 H:DA236 4.3 3.6 0.6 N7 D:DA36 4.3 3.1 0.4 C5 D:DC38 4.3 21.4 0.4 C2' H:DA236 4.3 11.3 0.6 C5 H:DC238 4.3 21.3 0.6 C2' D:DA36 4.4 10.3 0.4 C4 H:DA236 4.5 3.3 0.6 C4 D:DA36 4.5 2.7 0.4 C5 H:DA236 4.5 1.1 0.6 C5 D:DA36 4.5 0.6 0.4 C1' H:DA236 4.6 9.9 0.6 C1' D:DA36 4.7 9.3 0.4 C1' H:UFP237 4.8 10.8 0.6 C6 G:DG223 4.8 7.8 0.6 C6 C:DG23 4.8 8.5 0.4 C1' D:DC37 4.9 13.5 0.4 O1P H:UFP237 4.9 18.5 0.6 C2 D:DC38 4.9 20.9 0.4 C2 H:DC238 4.9 20.9 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