Fluorine in PDB 3sd8: Crystal Structure of Ara-Fhna Decamer Dna

The structure of Crystal Structure of Ara-Fhna Decamer Dna, PDB code: 3sd8 was solved by M.Egli, P.S.Pallan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.30 / 1.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.003, 42.855, 45.833, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23.8

The structure of Crystal Structure of Ara-Fhna Decamer Dna also contains other interesting chemical elements:

Strontium

(Sr)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Ara-Fhna Decamer Dna (pdb code 3sd8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Ara-Fhna Decamer Dna, PDB code: 3sd8:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Ara-Fhna Decamer Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Ara-Fhna Decamer Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:F106 b:32.8 occ:1.00 F3' A:F4H106 0.0 32.8 1.0 C3' A:F4H106 1.4 30.8 1.0 C2' A:F4H106 2.4 27.5 1.0 C4' A:F4H106 2.4 31.2 1.0 N1 A:F4H106 2.7 26.2 1.0 O4' A:DA107 2.8 29.6 1.0 O4' A:F4H106 2.9 36.3 1.0 C2 A:F4H106 3.0 26.0 1.0 O2 A:F4H106 3.1 27.2 1.0 O5' A:DA107 3.1 34.1 1.0 C8 A:DA107 3.1 24.2 1.0 C5' A:DA107 3.3 33.1 1.0 P A:DA107 3.5 31.7 1.0 C6 A:F4H106 3.6 24.9 1.0 N9 A:DA107 3.6 26.5 1.0 C4' A:DA107 3.6 31.2 1.0 C1' A:DA107 3.7 28.3 1.0 C1' A:F4H106 3.7 27.3 1.0 C5' A:F4H106 3.8 28.8 1.0 N7 A:DA107 4.0 23.4 1.0 OP2 A:DA107 4.0 36.6 1.0 N3 A:F4H106 4.0 24.9 1.0 O5' A:F4H106 4.1 30.4 1.0 C5 A:F4H106 4.5 22.3 1.0 C3' A:DA107 4.6 31.8 1.0 C4 A:F4H106 4.7 22.0 1.0 C4 A:DA107 4.7 24.6 1.0 OP1 A:DA107 4.8 33.8 1.0 C5 A:DA107 4.8 23.0 1.0 C2' A:DA107 4.9 29.3 1.0 C6' A:F4H106 5.0 31.4 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Ara-Fhna Decamer Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Ara-Fhna Decamer Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:F206 b:29.4 occ:1.00 F3' B:F4H206 0.0 29.4 1.0 C3' B:F4H206 1.4 30.2 1.0 C2' B:F4H206 2.3 27.2 1.0 C4' B:F4H206 2.4 27.9 1.0 N1 B:F4H206 2.7 23.2 1.0 O4' B:DA207 2.8 29.1 1.0 O4' B:F4H206 2.9 30.0 1.0 O5' B:DA207 3.0 33.8 1.0 C2 B:F4H206 3.1 24.1 1.0 O2 B:F4H206 3.1 27.0 1.0 C8 B:DA207 3.1 25.9 1.0 C5' B:DA207 3.5 31.7 1.0 P B:DA207 3.5 32.5 1.0 C6 B:F4H206 3.5 24.6 1.0 N9 B:DA207 3.6 25.9 1.0 C1' B:F4H206 3.7 28.8 1.0 C5' B:F4H206 3.7 27.6 1.0 C4' B:DA207 3.7 31.2 1.0 C1' B:DA207 3.7 25.0 1.0 N7 B:DA207 3.9 21.9 1.0 OP2 B:DA207 4.0 35.3 1.0 N3 B:F4H206 4.1 23.0 1.0 O5' B:F4H206 4.1 29.2 1.0 C5 B:F4H206 4.5 21.4 1.0 O B:HOH28 4.5 37.7 1.0 C4 B:DA207 4.6 22.4 1.0 C3' B:DA207 4.6 32.4 1.0 C4 B:F4H206 4.7 21.4 1.0 OP1 B:DA207 4.7 33.1 1.0 C5 B:DA207 4.7 20.3 1.0 C6' B:F4H206 4.8 29.9 1.0 C2' B:DA207 4.9 29.2 1.0

M.Egli, P.S.Pallan, C.R.Allerson, T.P.Prakash, A.Berdeja, J.Yu, B.Bhat, E.E.Swayze, P.Seth. Structural Origins of Opposite Effects on Stability By Axial and Equatorial 3'-Fluoro Modifications of Hexitol Nucleic Acid (Hna) To Be Published.