Magnesium in PDB 388d: Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability

The structure of Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability, PDB code: 388d was solved by I.Berger, V.Tereshko, H.Ikeda, V.E.Marquez, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.930, 39.820, 65.620, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / n/a

The structure of Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability (pdb code 388d). 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 B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability, PDB code: 388d:

Magnesium binding site 1 out of 1 in the Crystal Structure of B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability


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 B-Dna with Incorporated 2'-Deoxy-2'- Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg25 b:17.4 occ:1.00 O A:HOH273 2.1 15.6 1.0 O A:HOH275 2.1 18.2 1.0 O A:HOH276 2.1 20.1 1.0 O B:HOH272 2.1 16.9 1.0 O B:HOH277 2.1 19.7 1.0 O A:HOH274 2.2 16.8 1.0 O B:HOH107 4.2 14.9 1.0 O A:HOH102 4.2 29.3 1.0 O B:HOH104 4.3 16.5 1.0 O A:HOH103 4.3 21.3 1.0 O6 B:DG22 4.3 15.3 1.0 O A:HOH212 4.4 21.4 1.0 C5 A:DC1 4.4 14.8 1.0 N7 A:DG2 4.4 14.0 1.0 O6 A:DG2 4.5 14.7 1.0 C6 A:DC1 4.7 10.7 1.0 O B:HOH156 4.9 19.3 1.0

I.Berger, V.Tereshko, H.Ikeda, V.E.Marquez, M.Egli. Crystal Structures of B-Dna with Incorporated 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymines: Implications of Conformational Preorganization For Duplex Stability. Nucleic Acids Res. V. 26 2473 1998.
ISSN: ISSN 0305-1048
PubMed: 9580702
DOI: 10.1093/NAR/26.10.2473