Fluorine in PDB 461d: A "Hydrat-Ion Spine" in A B-Dna Minor Groove

The structure of A "Hydrat-Ion Spine" in A B-Dna Minor Groove, PDB code: 461d was solved by V.Tereshko, G.Minasov, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.070, 39.720, 65.770, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / n/a

The structure of A "Hydrat-Ion Spine" in A B-Dna Minor Groove also contains other interesting chemical elements:

Rubidium	(Rb)	1 atom
Magnesium	(Mg)	2 atoms

The binding sites of Fluorine atom in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove (pdb code 461d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove, PDB code: 461d:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of A "Hydrat-Ion Spine" in A B-Dna Minor Groove within 5.0Å range: probe atom residue distance (Å) B Occ A:F7 b:20.4 occ:1.00 F2' A:TAF7 0.0 20.4 1.0 C2' A:TAF7 1.3 18.4 1.0 C1' A:TAF7 2.3 17.7 1.0 C3' A:TAF7 2.4 18.6 1.0 N1 A:TAF7 2.7 17.1 1.0 C6 A:TAF7 2.9 17.2 1.0 C7 A:DT8 2.9 19.5 1.0 O4' A:TAF7 3.0 18.7 1.0 O A:HOH118 3.2 26.7 1.0 C4' A:TAF7 3.3 18.9 1.0 O A:HOH113 3.3 26.8 1.0 C6 A:DT8 3.4 18.3 1.0 C5 A:DT8 3.4 17.4 1.0 O A:HOH106 3.4 19.4 1.0 O3' A:TAF7 3.5 21.8 1.0 OP2 A:DT8 3.7 23.2 1.0 C2 A:TAF7 3.7 16.4 1.0 O5' A:TAF7 3.9 19.2 1.0 C5 A:TAF7 4.0 16.2 1.0 P A:DT8 4.0 22.5 1.0 O5' A:DT8 4.1 22.0 1.0 C5' A:TAF7 4.2 20.0 1.0 O2 A:TAF7 4.3 19.3 1.0 O4' A:DT8 4.4 20.1 1.0 N1 A:DT8 4.5 18.5 1.0 C4 A:DT8 4.5 17.8 1.0 N3 A:TAF7 4.6 16.2 1.0 C4 A:TAF7 4.8 15.7 1.0 C5M A:TAF7 4.8 18.4 1.0 O A:HOH142 4.8 30.5 1.0 C5' A:DT8 4.8 19.4 1.0

Fluorine binding site 2 out of 2 in the A "Hydrat-Ion Spine" in A B-Dna Minor Groove


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of A "Hydrat-Ion Spine" in A B-Dna Minor Groove within 5.0Å range: probe atom residue distance (Å) B Occ B:F19 b:22.6 occ:1.00 F2' B:TAF19 0.0 22.6 1.0 C2' B:TAF19 1.3 23.9 1.0 C1' B:TAF19 2.3 20.3 1.0 C3' B:TAF19 2.4 24.0 1.0 N1 B:TAF19 2.7 20.9 1.0 C6 B:TAF19 2.9 22.1 1.0 O4' B:TAF19 2.9 20.9 1.0 C7 B:DT20 3.0 23.3 1.0 C4' B:TAF19 3.3 22.0 1.0 O B:HOH132 3.4 30.3 1.0 O B:HOH137 3.4 31.7 1.0 C6 B:DT20 3.5 20.5 1.0 C5 B:DT20 3.5 21.6 1.0 O3' B:TAF19 3.5 24.3 1.0 O B:HOH163 3.6 46.2 1.0 OP2 B:DT20 3.7 28.5 1.0 O5' B:TAF19 3.8 26.8 1.0 C2 B:TAF19 3.8 20.0 1.0 C5 B:TAF19 4.0 19.5 1.0 P B:DT20 4.1 27.0 1.0 O5' B:DT20 4.2 25.8 1.0 C5' B:TAF19 4.2 23.2 1.0 O2 B:TAF19 4.4 21.4 1.0 O4' B:DT20 4.5 22.5 1.0 N1 B:DT20 4.6 22.6 1.0 N3 B:TAF19 4.7 19.7 1.0 C4 B:DT20 4.8 22.5 1.0 C5M B:TAF19 4.8 22.6 1.0 O A:HOH184 4.8 51.3 1.0 C4 B:TAF19 4.9 19.6 1.0 C5' B:DT20 4.9 24.0 1.0

V.Tereshko, G.Minasov, M.Egli. A "Hydrat-Ion Spine" in A B-Dna Minor Groove J.Am.Chem.Soc. V. 121 3590 1999.
ISSN: ISSN 0002-7863