Calcium in PDB 1zf0: B-Dna

The structure of B-Dna, PDB code: 1zf0 was solved by F.A.Hays, A.T.Teegarden, Z.J.R.Jones, M.Harms, D.Raup, J.Watson, E.Cavaliere, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.17 / 1.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	33.290, 33.290, 93.620, 90.00, 90.00, 120.00
R / Rfree (%)	25.3 / 25.8

The binding sites of Calcium atom in the B-Dna (pdb code 1zf0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the B-Dna, PDB code: 1zf0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca21 b:1.9 occ:1.00 O A:HOH27 2.3 1.0 1.0 O B:HOH33 2.3 1.0 1.0 O B:HOH34 2.4 2.3 1.0 O B:HOH48 2.4 3.9 1.0 O A:HOH112 2.5 1.0 1.0 O B:HOH76 2.7 3.9 1.0 N2 A:DG3 4.2 1.9 1.0 O4' B:DG20 4.4 1.9 1.0 O4' A:DT4 4.5 2.6 1.0 O A:HOH63 4.5 1.0 1.0 N3 A:DG3 4.7 2.0 1.0 O B:HOH166 4.7 1.2 1.0 N2 B:DG19 4.7 2.2 1.0 C5' B:DG20 4.8 1.9 1.0 C4' B:DG20 4.8 2.0 1.0 O B:HOH169 4.8 5.2 1.0 C4' A:DT4 4.8 2.6 1.0 C2 A:DG3 4.8 2.0 1.0 N3 B:DG19 4.8 2.1 1.0 O B:HOH80 5.0 2.7 1.0

Calcium binding site 2 out of 4 in the B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca30 b:1.0 occ:0.50 OP2 A:DC8 2.2 1.9 1.0 O A:HOH65 2.3 3.4 1.0 O A:HOH109 2.7 8.8 0.5 P A:DC8 3.4 1.9 1.0 OP1 A:DC8 3.8 1.8 1.0 C2' A:DA7 4.3 1.7 1.0 O3' A:DA7 4.4 1.8 1.0 C3' A:DA7 4.4 1.9 1.0 O5' A:DC8 4.5 1.9 1.0 O A:HOH117 4.9 8.6 1.0 O A:HOH22 4.9 4.1 1.0

Calcium binding site 3 out of 4 in the B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca25 b:1.0 occ:1.00 O B:HOH108 2.2 3.2 1.0 O B:HOH50 2.4 1.0 1.0 O B:HOH44 2.6 1.0 1.0 O B:HOH125 4.3 6.2 1.0 OP2 B:DG20 4.3 1.6 1.0

Calcium binding site 4 out of 4 in the B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca49 b:1.0 occ:1.00 O B:HOH60 2.3 1.0 1.0 O A:HOH75 2.3 1.0 1.0 O A:HOH29 2.4 1.0 1.0 O A:HOH28 2.5 1.0 1.0 O A:HOH86 2.5 1.0 1.0 O B:HOH46 2.6 9.3 1.0 O B:HOH161 4.2 2.5 1.0 N2 B:DG13 4.2 1.8 1.0 O A:HOH126 4.3 2.8 1.0 C4' B:DT14 4.4 2.1 1.0 O A:HOH120 4.5 8.0 1.0 C5' B:DT14 4.6 2.1 1.0 O4' A:DG10 4.6 2.2 1.0 O4' A:DG9 4.6 2.4 1.0 N3 B:DG13 4.7 1.9 1.0 O4' B:DT14 4.7 2.2 1.0 N3 A:DG9 4.8 2.2 1.0 C2 B:DG13 5.0 1.9 1.0 N2 A:DG9 5.0 2.0 1.0 C4' A:DG9 5.0 2.3 1.0

F.A.Hays, A.Teegarden, Z.J.Jones, M.Harms, D.Raup, J.Watson, E.Cavaliere, P.S.Ho. How Sequence Defines Structure: A Crystallographic Map of Dna Structure and Conformation. Proc.Natl.Acad.Sci.Usa V. 102 7157 2005.
ISSN: ISSN 0027-8424
PubMed: 15870206
DOI: 10.1073/PNAS.0409455102