Fluorine in PDB 1y8l: Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*)

The structure of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*), PDB code: 1y8l was solved by M.Egli, G.Minasov, V.Tereshko, P.S.Pallan, M.Teplova, G.B.Inamati, E.A.Lesnik, S.R.Owens, B.S.Ross, T.P.Prakash, M.Manoharan, 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 (°)	24.636, 45.020, 45.132, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.2

The structure of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*) (pdb code 1y8l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*), PDB code: 1y8l:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*)


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 the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*) within 5.0Å range: probe atom residue distance (Å) B Occ A:F6 b:26.9 occ:1.00 FD' A:TFE6 0.0 26.9 1.0 CC' A:TFE6 1.3 24.3 1.0 FE' A:TFE6 2.1 27.5 1.0 FF' A:TFE6 2.2 28.1 1.0 CB' A:TFE6 2.3 19.5 1.0 O A:HOH176 3.5 23.9 1.0 O2' A:TFE6 3.5 16.9 1.0 O A:HOH112 4.4 23.3 1.0 O4' A:DA7 4.4 15.2 1.0 C2' A:TFE6 4.7 14.7 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*)


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 the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*) within 5.0Å range: probe atom residue distance (Å) B Occ A:F6 b:27.5 occ:1.00 FE' A:TFE6 0.0 27.5 1.0 CC' A:TFE6 1.3 24.3 1.0 FF' A:TFE6 2.1 28.1 1.0 FD' A:TFE6 2.1 26.9 1.0 CB' A:TFE6 2.3 19.5 1.0 O2' A:TFE6 2.7 16.9 1.0 C5' A:DA7 3.5 13.8 1.0 O4' A:DA7 3.6 15.2 1.0 C4' A:DA7 3.7 12.5 1.0 C2' A:TFE6 4.0 14.7 1.0 O A:HOH138 4.0 26.7 0.5 O3' A:TFE6 4.4 16.9 1.0 O5' A:DA7 4.5 14.8 1.0 O A:HOH176 4.6 23.9 1.0 C3' A:TFE6 4.8 17.2 1.0 C1' A:DA7 4.9 12.2 1.0 C1' A:TFE6 5.0 15.9 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*) within 5.0Å range: probe atom residue distance (Å) B Occ A:F6 b:28.1 occ:1.00 FF' A:TFE6 0.0 28.1 1.0 CC' A:TFE6 1.3 24.3 1.0 FE' A:TFE6 2.1 27.5 1.0 FD' A:TFE6 2.2 26.9 1.0 CB' A:TFE6 2.3 19.5 1.0 O2' A:TFE6 2.8 16.9 1.0 O A:HOH182 3.5 36.3 1.0 O A:HOH112 3.5 23.3 1.0 O A:HOH138 4.0 26.7 0.5 C2' A:TFE6 4.1 14.7 1.0 C1' A:TFE6 4.6 15.9 1.0 C4' A:TFE6 4.7 18.0 1.0 C3' A:TFE6 4.9 17.2 1.0 O4' A:TFE6 4.9 17.3 1.0 O3' A:TFE6 4.9 16.9 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*) within 5.0Å range: probe atom residue distance (Å) B Occ B:F16 b:24.4 occ:1.00 FD' B:TFE16 0.0 24.4 1.0 CC' B:TFE16 1.3 25.8 1.0 FF' B:TFE16 2.1 26.6 1.0 FE' B:TFE16 2.2 26.5 1.0 CB' B:TFE16 2.3 21.9 1.0 O2' B:TFE16 2.7 20.6 1.0 O B:HOH142 3.2 37.2 1.0 O B:HOH143 3.4 20.6 0.5 O B:HOH148 4.0 34.9 1.0 C2' B:TFE16 4.1 16.6 1.0 C1' B:TFE16 4.5 18.8 1.0 C4' B:TFE16 4.8 19.0 1.0 C3' B:TFE16 4.9 20.1 1.0 O4' B:TFE16 4.9 18.2 1.0 O3' B:TFE16 5.0 22.4 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*) within 5.0Å range: probe atom residue distance (Å) B Occ B:F16 b:26.5 occ:1.00 FE' B:TFE16 0.0 26.5 1.0 CC' B:TFE16 1.3 25.8 1.0 FF' B:TFE16 2.1 26.6 1.0 FD' B:TFE16 2.2 24.4 1.0 CB' B:TFE16 2.3 21.9 1.0 O2' B:TFE16 2.7 20.6 1.0 O B:HOH142 3.2 37.2 1.0 C5' B:DA17 3.6 17.9 1.0 O B:HOH151 3.6 43.6 1.0 O4' B:DA17 3.8 18.0 1.0 O B:HOH148 3.8 34.9 1.0 C4' B:DA17 3.8 16.6 1.0 C2' B:TFE16 3.9 16.6 1.0 O3' B:TFE16 4.3 22.4 1.0 O B:HOH143 4.5 20.6 0.5 O5' B:DA17 4.6 21.9 1.0 C3' B:TFE16 4.7 20.1 1.0 C1' B:TFE16 4.9 18.8 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*) within 5.0Å range: probe atom residue distance (Å) B Occ B:F16 b:26.6 occ:1.00 FF' B:TFE16 0.0 26.6 1.0 CC' B:TFE16 1.3 25.8 1.0 FD' B:TFE16 2.1 24.4 1.0 FE' B:TFE16 2.1 26.5 1.0 CB' B:TFE16 2.3 21.9 1.0 O B:HOH151 3.5 43.6 1.0 O2' B:TFE16 3.5 20.6 1.0 O4' B:DA17 4.5 18.0 1.0 C2' B:TFE16 4.7 16.6 1.0 O B:HOH142 4.8 37.2 1.0 O B:HOH148 4.9 34.9 1.0

M.Egli, G.Minasov, V.Tereshko, P.S.Pallan, M.Teplova, G.B.Inamati, E.A.Lesnik, S.R.Owens, B.S.Ross, T.P.Prakash, M.Manoharan. Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the Rna Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications. Biochemistry V. 44 9045 2005.
ISSN: ISSN 0006-2960
PubMed: 15966728
DOI: 10.1021/BI050574M