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Fluorine in PDB 3v07: Crystal Structure of R-6'-Me-3'-Fluoro Hexitol Nucleic Acid

Protein crystallography data

The structure of Crystal Structure of R-6'-Me-3'-Fluoro Hexitol Nucleic Acid, PDB code: 3v07 was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.45 / 1.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 27.302, 43.481, 45.530, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of R-6'-Me-3'-Fluoro Hexitol Nucleic Acid (pdb code 3v07). 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 R-6'-Me-3'-Fluoro Hexitol Nucleic Acid, PDB code: 3v07:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3v07

Go back to Fluorine Binding Sites List in 3v07
Fluorine binding site 1 out of 2 in the Crystal Structure of R-6'-Me-3'-Fluoro Hexitol Nucleic Acid


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 R-6'-Me-3'-Fluoro Hexitol Nucleic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F106

b:18.7
occ:1.00
F3' A:F6H106 0.0 18.7 1.0
C3' A:F6H106 1.4 16.6 1.0
C2' A:F6H106 2.3 15.9 1.0
C4' A:F6H106 2.4 16.3 1.0
O4' A:F6H106 2.8 21.3 1.0
C5' A:F6H106 2.9 17.8 1.0
C1' A:F6H106 2.9 17.5 1.0
O5' A:F6H106 3.4 16.4 1.0
C5' A:DA107 3.5 19.9 1.0
O4' A:DA107 3.6 17.2 1.0
N1 A:F6H106 3.6 14.6 1.0
O5' A:DA107 3.7 19.6 1.0
P A:DA107 4.0 20.8 1.0
C4' A:DA107 4.1 18.5 1.0
O2 A:F6H106 4.2 15.8 1.0
C2 A:F6H106 4.3 14.0 1.0
C6' A:F6H106 4.3 18.1 1.0
C6 A:F6H106 4.5 15.2 1.0
C1' A:DA107 4.8 17.0 1.0
OP1 A:DA107 4.9 24.1 1.0
OP2 A:DA107 4.9 21.6 1.0
C8 A:DA107 5.0 15.9 1.0
C7' A:F6H106 5.0 19.9 1.0

Fluorine binding site 2 out of 2 in 3v07

Go back to Fluorine Binding Sites List in 3v07
Fluorine binding site 2 out of 2 in the Crystal Structure of R-6'-Me-3'-Fluoro Hexitol Nucleic Acid


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 R-6'-Me-3'-Fluoro Hexitol Nucleic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F206

b:17.9
occ:1.00
F3' B:F6H206 0.0 17.9 1.0
C3' B:F6H206 1.4 16.6 1.0
C2' B:F6H206 2.3 15.4 1.0
C4' B:F6H206 2.4 16.5 1.0
O4' B:F6H206 2.8 18.3 1.0
C5' B:F6H206 2.9 17.5 1.0
C1' B:F6H206 2.9 15.9 1.0
O5' B:F6H206 3.4 16.9 1.0
O4' B:DA207 3.5 17.4 1.0
C5' B:DA207 3.5 18.3 1.0
N1 B:F6H206 3.6 14.4 1.0
O5' B:DA207 3.8 17.8 1.0
O B:HOH322 3.8 31.8 1.0
P B:DA207 3.9 19.4 1.0
C4' B:DA207 4.1 18.3 1.0
O2 B:F6H206 4.3 16.8 1.0
C2 B:F6H206 4.4 15.0 1.0
C6' B:F6H206 4.4 19.4 1.0
C6 B:F6H206 4.5 15.2 1.0
O B:HOH321 4.7 32.8 1.0
C1' B:DA207 4.8 15.9 1.0
OP2 B:DA207 4.8 22.7 1.0
C7' B:F6H206 4.8 20.2 1.0
OP1 B:DA207 4.8 21.0 1.0
C8 B:DA207 4.9 16.7 1.0

Reference:

P.S.Pallan, J.Yu, C.R.Allerson, E.E.Swayze, P.Seth, M.Egli. Insights From Crystal Structures Into the Opposite Effects on Rna Affinity Caused By the S- and R-6'-Methyl Backbone Modifications of 3'-Fluoro Hexitol Nucleic Acid. Biochemistry V. 51 7 2012.
ISSN: ISSN 0006-2960
PubMed: 22229409
DOI: 10.1021/BI201810R
Page generated: Sun Dec 13 11:56:46 2020

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