Calcium in PDB 1zf6: Tgg Duplex A-Dna

The structure of Tgg Duplex A-Dna, PDB code: 1zf6 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)	15.95 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.239, 41.179, 44.410, 90.00, 90.00, 90.00
R / Rfree (%)	25.6 / 30.6

The structure of Tgg Duplex A-Dna also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Tgg Duplex A-Dna (pdb code 1zf6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Tgg Duplex A-Dna, PDB code: 1zf6:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tgg Duplex A-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tgg Duplex A-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca22 b:2.2 occ:1.00 O A:HOH47 2.3 7.1 1.0 O A:HOH35 2.3 5.9 1.0 O A:HOH38 2.3 3.4 1.0 O A:HOH50 2.4 3.3 1.0 O A:HOH21 2.6 2.1 1.0 O A:HOH36 2.6 2.6 1.0 O A:HOH67 3.9 14.3 1.0 O6 A:DG8 4.1 2.4 1.0 O A:HOH32 4.2 4.2 1.0 O A:HOH118 4.3 22.1 1.0 N7 A:DG8 4.4 2.0 1.0 N7 A:DG7 4.4 2.1 1.0 O A:HOH98 4.7 4.2 1.0 O A:HOH55 4.8 11.9 1.0 O6 A:DG7 4.9 2.0 1.0 C6 A:DG8 5.0 2.5 1.0

Calcium binding site 2 out of 3 in the Tgg Duplex A-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tgg Duplex A-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca24 b:2.0 occ:1.00 OP1 A:DG10 2.3 2.0 1.0 O A:HOH52 2.4 4.3 1.0 O A:HOH53 2.4 6.2 1.0 O A:HOH33 2.4 2.0 1.0 O A:HOH40 2.5 2.0 1.0 P A:DG10 3.7 2.3 1.0 C5' A:DG10 4.1 2.4 1.0 O A:HOH58 4.2 8.9 1.0 O5' A:DG10 4.3 2.0 1.0 O3' A:DG9 4.3 3.7 1.0 O A:HOH70 4.3 15.9 1.0 OP2 A:DG10 4.8 2.0 1.0 O A:HOH107 4.9 9.6 1.0

Calcium binding site 3 out of 3 in the Tgg Duplex A-Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tgg Duplex A-Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca25 b:2.5 occ:1.00 OP1 B:DC12 2.3 3.0 1.0 O B:HOH54 2.4 7.3 1.0 O B:HOH42 2.4 2.0 1.0 OP1 A:DC2 2.5 6.8 1.0 O B:HOH81 2.7 8.6 1.0 O B:HOH100 3.0 13.7 1.0 O A:HOH80 3.3 11.8 1.0 P B:DC12 3.5 2.8 1.0 P A:DC2 3.6 4.8 1.0 OP2 B:DC12 3.9 5.1 1.0 OP2 A:DC2 4.0 6.5 1.0 O B:HOH43 4.3 13.8 1.0 O5' B:DC12 4.3 2.0 1.0 O A:HOH121 4.4 13.5 1.0 O5' A:DC2 4.5 4.1 1.0 O A:HOH59 4.5 7.9 1.0 O B:HOH85 4.6 26.2 1.0 O3' B:DC11 4.7 3.3 1.0 OP2 B:DC13 4.8 5.4 1.0 OP2 A:DC3 4.8 5.7 1.0 C5' B:DC12 4.8 2.4 1.0 O3' A:DC1 4.8 4.5 1.0 O B:HOH72 4.8 14.6 1.0 C5' A:DC2 5.0 6.1 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