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

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

Resolution Low / High (Å)	30.59 / 1.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.968, 24.542, 37.992, 90.00, 111.98, 90.00
R / Rfree (%)	24.8 / 27.8

The binding sites of Calcium atom in the Crystal Structure of Holliday Junctions Stabilized By 5-Methylcytosine in Gcc Junction Core (pdb code 5dsa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Holliday Junctions Stabilized By 5-Methylcytosine in Gcc Junction Core, PDB code: 5dsa:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Holliday Junctions Stabilized By 5-Methylcytosine 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-Methylcytosine in Gcc Junction Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:19.9 occ:0.60 CA A:CA102 2.0 25.9 0.4 O A:HOH237 2.2 28.2 1.0 O A:HOH221 2.4 22.5 1.0 O A:HOH210 2.5 20.8 1.0 O A:HOH244 3.9 27.4 1.0 O4' A:DG3 4.1 21.3 1.0 O A:HOH218 4.2 28.7 1.0 O A:HOH208 4.5 23.7 1.0 N3 A:DG3 4.5 20.9 1.0 O A:HOH212 4.6 23.4 1.0 C4' A:DG3 4.6 21.6 1.0 O2 A:DC2 4.8 18.7 1.0 O4' A:DG4 4.8 21.3 1.0 N2 A:DG3 4.8 20.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Holliday Junctions Stabilized By 5-Methylcytosine in Gcc Junction Core


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 Holliday Junctions Stabilized By 5-Methylcytosine in Gcc Junction Core within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:25.9 occ:0.40 CA A:CA101 2.0 19.9 0.6 O A:HOH210 2.5 20.8 1.0 O A:HOH244 2.5 27.4 1.0 O A:HOH208 2.7 23.7 1.0 O A:HOH237 4.1 28.2 1.0 O A:HOH221 4.1 22.5 1.0 O2 A:DC2 4.2 18.7 1.0 O4' A:DG3 4.6 21.3 1.0 O4' A:DC2 4.8 19.9 1.0 O A:HOH218 4.9 28.7 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