Calcium in PDB 5dsb: Crystal Structure of Holliday Junctions Stabilized By 5- Hydroxymethylcytosine in Gcc Junction Core

The structure of Crystal Structure of Holliday Junctions Stabilized By 5- Hydroxymethylcytosine in Gcc Junction Core, PDB code: 5dsb was solved by C.M.Vander Zanden, R.K.Rowe, A.J.Broad, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.34 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.073, 24.768, 38.061, 90.00, 111.82, 90.00
R / Rfree (%)	25.1 / 28.8

The binding sites of Calcium atom in the Crystal Structure of Holliday Junctions Stabilized By 5- Hydroxymethylcytosine in Gcc Junction Core (pdb code 5dsb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Holliday Junctions Stabilized By 5- Hydroxymethylcytosine in Gcc Junction Core, PDB code: 5dsb:

Calcium binding site 1 out of 1 in the Crystal Structure of Holliday Junctions Stabilized By 5- Hydroxymethylcytosine in Gcc Junction Core


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 Holliday Junctions Stabilized By 5- Hydroxymethylcytosine in Gcc Junction Core within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:21.2 occ:0.75 O B:HOH243 2.2 23.2 1.0 O B:HOH237 2.3 28.7 1.0 O B:HOH236 2.3 28.9 1.0 O B:HOH223 2.5 17.3 1.0 O B:HOH216 2.7 19.8 1.0 O4' B:DG13 4.2 19.4 1.0 O B:HOH244 4.3 25.0 1.0 O B:HOH228 4.4 21.0 1.0 O B:HOH227 4.5 25.5 1.0 C4' B:DG13 4.6 19.7 1.0 N3 B:DG13 4.7 16.0 1.0 O B:HOH206 4.7 30.6 1.0 O2 B:DC12 4.9 16.3 1.0 O4' B:DG14 4.9 18.7 1.0 N2 B:DG13 4.9 16.4 1.0

C.M.Vander Zanden, R.K.Rowe, A.J.Broad, A.B.Robertson, P.S.Ho. Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions. Biochemistry V. 55 5781 2016.
ISSN: ISSN 1520-4995
PubMed: 27653243
DOI: 10.1021/ACS.BIOCHEM.6B00801