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

Protein crystallography data

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

Fluorine Binding Sites:

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 1y86

Go back to Fluorine Binding Sites List in 1y86
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 1y86

Go back to Fluorine Binding Sites List in 1y86
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

Reference:

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
Page generated: Sun Dec 13 11:34:14 2020

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