Fluorine in PDB 1y86: Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Fluoro)Ethyl] Thymidine (T*)

The structure of Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Fluoro)Ethyl] Thymidine (T*), PDB code: 1y86 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 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.263, 44.184, 45.392, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 18.9

The binding sites of Fluorine atom in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Fluoro)Ethyl] Thymidine (T*) (pdb code 1y86). 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 the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Fluoro)Ethyl] Thymidine (T*), PDB code: 1y86:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Fluoro)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- (Fluoro)Ethyl] Thymidine (T*) within 5.0Å range: probe atom residue distance (Å) B Occ A:F6 b:29.0 occ:1.00 FC' A:1256 0.0 29.0 1.0 CB' A:1256 1.4 26.9 1.0 CA' A:1256 2.4 20.0 1.0 O A:HOH200 2.7 35.0 0.5 O2' A:1256 2.9 19.8 1.0 O A:HOH184 3.4 23.9 0.5 C5' A:DA7 3.5 19.8 1.0 O A:HOH185 3.6 41.9 0.5 O4' A:DA7 3.8 19.6 1.0 C4' A:DA7 3.8 19.0 1.0 C2' A:1256 4.2 18.0 1.0 O A:HOH188 4.4 34.4 0.5 O3' A:1256 4.6 23.4 1.0 O5' A:DA7 4.7 19.6 1.0 O A:HOH129 4.8 24.9 1.0 O A:HOH191 4.9 32.0 0.5 C3' A:1256 5.0 20.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Fluoro)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- (Fluoro)Ethyl] Thymidine (T*) within 5.0Å range: probe atom residue distance (Å) B Occ B:F16 b:33.3 occ:1.00 FC' B:12516 0.0 33.3 1.0 CB' B:12516 1.4 28.8 1.0 CA' B:12516 2.3 25.4 1.0 O B:HOH198 2.7 37.7 0.5 O2' B:12516 2.8 22.8 1.0 O B:HOH153 2.9 45.6 1.0 O B:HOH117 3.2 33.9 1.0 C5' B:DA17 3.9 21.8 1.0 O B:HOH168 4.0 38.5 1.0 O B:HOH178 4.0 34.6 0.5 O4' B:DA17 4.1 23.6 1.0 C2' B:12516 4.2 20.2 1.0 C4' B:DA17 4.2 20.9 1.0 O3' B:12516 4.7 24.3 1.0 O5' B:DA17 4.9 21.2 1.0 C3' B:12516 5.0 20.8 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