Magnesium 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:

Fluorine

(F)

6 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the A-Dna Gcgtat*Cgc with A 2'-O-[2- (Trifluoro)Ethyl] Thymidine (T*), PDB code: 1y8l:

Magnesium binding site 1 out of 1 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 Magnesium with other atoms in the Mg 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:Mg101 b:36.4 occ:1.00 O A:HOH104 1.9 29.7 1.0 O A:HOH107 2.0 27.3 0.5 O A:HOH102 2.0 23.8 1.0 O A:HOH106 2.1 24.0 0.5 O B:HOH105 2.2 25.4 0.5 O A:HOH103 2.3 26.2 1.0 O A:HOH107 3.2 23.5 0.5 O6 A:DG3 3.9 14.3 1.0 O B:HOH129 4.0 29.4 1.0 O A:HOH198 4.0 30.2 0.5 N7 A:DG3 4.2 10.5 1.0 O A:HOH188 4.5 46.6 1.0 O A:HOH117 4.5 20.8 1.0 O4 A:DT4 4.5 10.3 1.0 O4 B:TFE16 4.6 13.3 1.0 C6 A:DG3 4.6 10.6 1.0 C5 A:DG3 4.8 11.5 1.0 N6 A:DA5 4.8 9.7 1.0 N6 B:DA17 4.9 11.3 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