Calcium in PDB 6m44: 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (High Cryoprotectant)

The structure of 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (High Cryoprotectant), PDB code: 6m44 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)	48.03 / 3.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.038, 218.595, 115.931, 90.00, 90.22, 90.00
R / Rfree (%)	20.8 / 28.6

The binding sites of Calcium atom in the 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (High Cryoprotectant) (pdb code 6m44). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (High Cryoprotectant), PDB code: 6m44:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:0.5 occ:1.00 OD1 E:ASP81 2.9 0.6 1.0 O3' I:DC241 3.9 0.6 1.0 CG E:ASP81 4.0 0.1 1.0 C4' I:DC241 4.3 0.1 1.0 C3' I:DC241 4.4 0.8 1.0 OD2 E:ASP81 4.5 0.5 1.0 OP1 I:DA242 4.6 0.5 1.0 NE E:ARG83 4.6 0.9 1.0 C5' I:DC241 4.7 0.3 1.0 NH2 E:ARG83 4.7 0.0 1.0 P I:DA242 4.8 0.1 1.0

Calcium binding site 2 out of 4 in the 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:0.0 occ:1.00 OE1 G:GLU91 2.9 0.6 1.0 CD G:GLU91 4.0 0.3 1.0 CB G:GLU91 4.0 0.9 1.0 O G:ASN89 4.1 0.9 1.0 CG G:GLU91 4.5 0.6 1.0 CA G:GLU91 4.6 0.5 1.0 N G:GLU91 4.7 0.3 1.0

Calcium binding site 3 out of 4 in the 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (High Cryoprotectant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (High Cryoprotectant) within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca401 b:0.9 occ:1.00 O6 I:DG136 2.5 0.5 1.0 C6 I:DG136 3.6 0.2 1.0 N7 I:DG136 4.2 0.6 1.0 O6 J:DG215 4.2 0.9 1.0 C5 I:DG136 4.2 0.1 1.0 N7 I:DG135 4.3 0.7 1.0 N4 J:DC216 4.5 0.7 1.0 C8 I:DG135 4.5 0.8 1.0 N1 I:DG136 4.7 0.6 1.0 N4 I:DC137 5.0 0.1 1.0

Calcium binding site 4 out of 4 in the 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (High Cryoprotectant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 355 Bp Di-Nucleosome Harboring Cohesive Dna Termini (High Cryoprotectant) within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca401 b:0.6 occ:1.00 C7 J:DT235 4.0 0.1 1.0 OP2 J:DT235 4.0 0.0 1.0 C2' J:DC234 4.7 1.0 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