Calcium in PDB 478d: Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine

The structure of Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine, PDB code: 478d was solved by G.Minasov, V.Tereshko, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.20
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	42.310, 42.310, 99.680, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 26.2

The structure of Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine (pdb code 478d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine, PDB code: 478d:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca112 b:41.9 occ:1.00 O B:HOH116 2.2 29.7 1.0 O B:HOH113 2.3 21.5 1.0 O A:HOH117 2.3 26.8 1.0 O A:HOH114 2.4 33.6 1.0 O A:HOH118 2.6 45.1 1.0 O B:HOH119 3.1 30.6 1.0 N2 A:DG4 3.9 25.5 1.0 O B:HOH188 3.9 32.4 0.5 O B:HOH123 4.1 30.6 1.0 O4' B:DG22 4.5 29.3 1.0 O2 B:DC21 4.5 27.3 1.0 O A:HOH218 4.5 48.7 0.5 C4' B:DG22 4.6 32.2 1.0 O4' A:DA6 4.8 31.9 1.0 O4' A:DA5 4.9 24.5 1.0 C5' A:DA6 4.9 32.8 1.0 C4' A:DA6 5.0 30.7 1.0 C5' B:DG22 5.0 33.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca120 b:34.4 occ:0.33 O A:HOH121 2.2 47.5 1.0 OP1 A:DA5 2.5 32.1 1.0 P A:DA5 3.7 30.8 1.0 OP2 A:DA5 4.2 32.1 1.0 O5' A:DA5 4.3 30.7 1.0 C5' A:DA5 4.7 30.2 1.0 O3' A:DG4 4.9 27.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the B-Dna Dodecamer 5'-D(Cgcgaa(Taf)Tcgcg), Where Taf Is 2'-Deoxy-2'-Fluoro-Arabino-Furanosyl Thymine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:34.7 occ:1.00 O B:HOH102 2.2 33.7 1.0 OP1 B:DG24 2.2 28.4 1.0 P B:DG24 3.4 27.0 1.0 O3' B:DC23 3.8 24.8 1.0 OP2 B:DG24 4.2 29.5 1.0 O5' B:DG24 4.6 28.8 1.0 C5' B:DG24 5.0 28.2 1.0

G.Minasov, V.Tereshko, M.Egli. Atomic-Resolution Crystal Structures of B-Dna Reveal Specific Influences of Divalent Metal Ions on Conformation and Packing. J.Mol.Biol. V. 291 83 1999.
ISSN: ISSN 0022-2836
PubMed: 10438608
DOI: 10.1006/JMBI.1999.2934