Calcium in PDB 1zf7: Gac Duplex B-Dna

The structure of Gac Duplex B-Dna, PDB code: 1zf7 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)	16.25 / 1.05
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	53.440, 53.440, 43.870, 90.00, 90.00, 120.00
R / Rfree (%)	27.6 / 28.8

The structure of Gac Duplex B-Dna also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Gac Duplex B-Dna (pdb code 1zf7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Gac Duplex B-Dna, PDB code: 1zf7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Gac Duplex B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Gac Duplex B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca22 b:3.2 occ:1.00 O A:HOH28 2.3 5.0 1.0 O A:HOH31 2.4 4.3 1.0 O A:HOH29 2.5 5.4 1.0 O A:HOH27 2.5 3.0 1.0 O A:HOH35 2.5 7.2 1.0 O A:HOH30 2.5 2.9 1.0 O A:HOH43 4.1 4.4 1.0 OP2 A:DT4 4.2 5.9 1.0 O A:HOH42 4.7 4.3 1.0

Calcium binding site 2 out of 3 in the Gac Duplex B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Gac Duplex B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca23 b:3.7 occ:1.00 OP2 A:DG3 2.3 5.0 1.0 O A:HOH32 2.5 4.8 1.0 P A:DG3 3.7 5.0 1.0 C2' A:DC2 4.0 10.5 1.0 N7 A:DG3 4.4 4.1 1.0 C8 A:DG3 4.4 3.9 1.0 C3' A:DC2 4.4 10.1 1.0 OP1 A:DG3 4.5 6.4 1.0 O3' A:DC2 4.6 7.9 1.0 O5' A:DG3 4.6 5.4 1.0

Calcium binding site 3 out of 3 in the Gac Duplex B-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Gac Duplex B-Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca21 b:2.3 occ:1.00 OP2 B:DC18 2.3 3.0 1.0 O B:HOH33 2.3 5.5 1.0 O B:HOH34 2.5 4.2 1.0 O B:HOH26 2.5 4.9 1.0 O B:HOH25 2.5 2.8 1.0 O B:HOH36 2.5 3.3 1.0 P B:DC18 3.7 3.3 1.0 O5' B:DC18 4.1 3.2 1.0 C2' B:DA17 4.2 2.8 1.0 C3' B:DA17 4.2 2.9 1.0 O3' B:DA17 4.5 2.2 1.0 O B:HOH41 4.7 2.6 1.0 OP1 B:DC18 4.8 3.0 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