Calcium in PDB 6m3v: 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini

The structure of 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini, PDB code: 6m3v was solved by Z.Adhireksan, D.Sharma, P.L.Lee, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.33 / 4.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.987, 228.970, 118.839, 90.00, 92.68, 90.00
R / Rfree (%)	20.5 / 26.1

The structure of 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Calcium atom in the 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (pdb code 6m3v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini, PDB code: 6m3v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca401 b:0.0 occ:1.00 N3 J:DG326 3.6 0.8 1.0 N2 J:DG326 3.6 0.4 1.0 N2 I:DG27 3.6 0.8 1.0 C2 J:DG326 4.0 0.8 1.0 O4' J:DG327 4.1 0.0 1.0 C5' J:DG327 4.2 0.9 1.0 C4' J:DG327 4.4 1.0 1.0 C2 I:DG27 4.6 0.3 1.0 C4 J:DG326 4.6 0.7 1.0 N3 I:DG27 4.8 0.9 1.0 O2 J:DC325 4.9 0.1 1.0 C1' J:DG326 4.9 0.8 1.0 O4' J:DG326 5.0 0.4 1.0

Calcium binding site 2 out of 2 in the 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini within 5.0Å range: probe atom residue distance (Å) B Occ M:Ca201 b:0.0 occ:1.00 OE1 M:GLU91 3.0 0.7 1.0 CD M:GLU91 4.0 0.8 1.0 CB M:GLU91 4.1 0.6 1.0 CG M:GLU91 4.4 0.6 1.0 OE2 M:GLU91 4.9 0.4 1.0

Z.Adhireksan, D.Sharma, P.L.Lee, C.A.Davey. Near-Atomic Resolution Structures of Interdigitated Nucleosome Fibres. Nat Commun V. 11 4747 2020.
ISSN: ESSN 2041-1723
PubMed: 32958761
DOI: 10.1038/S41467-020-18533-2