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Calcium in PDB 6la8: 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0

Protein crystallography data

The structure of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0, PDB code: 6la8 was solved by Z.Adhireksan, P.L.Lee, D.Sharma, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.32 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.055, 184.073, 223.367, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26.5

Other elements in 6la8:

The structure of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 also contains other interesting chemical elements:

Potassium (K) 7 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Calcium atom in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (pdb code 6la8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 23 binding sites of Calcium where determined in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0, PDB code: 6la8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 23 in 6la8

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Calcium binding site 1 out of 23 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:1.0
occ:1.00
 CE1 G:TYR57 4.4 0.5 1.0
CD1 G:TYR57 4.7 0.6 1.0
OE1 G:GLU61 4.9 0.3 1.0
CB G:ALA60 4.9 0.2 1.0

Calcium binding site 2 out of 23 in 6la8

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Calcium binding site 2 out of 23 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca401

b:0.2
occ:1.00
 O4' I:DC264 4.1 0.7 1.0
C5' I:DT265 4.2 0.7 1.0
O2 I:DC264 4.3 0.0 1.0
N3 J:DA83 4.5 0.5 1.0
C4' I:DT265 4.5 0.8 1.0
O4' I:DT265 4.6 1.0 1.0
C4' J:DC84 4.7 0.1 1.0
O4' J:DC84 4.7 0.9 1.0
C2 J:DA83 4.8 0.0 1.0
C4' I:DC264 4.8 0.3 1.0
C5' J:DC84 4.9 0.8 1.0

Calcium binding site 3 out of 23 in 6la8

Go back to Calcium Binding Sites List in 6la8
Calcium binding site 3 out of 23 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca402

b:0.3
occ:1.00
 C5' I:DG142 3.9 0.8 1.0
C4' I:DG142 4.1 1.0 1.0
C4' J:DA207 4.3 0.4 1.0
O4' I:DG142 4.4 0.2 1.0
C5' J:DA207 4.6 0.3 1.0
O4' J:DA207 4.7 0.8 1.0
O4' I:DT141 4.8 0.4 1.0
N2 I:DG140 4.9 0.6 1.0
O2 J:DC206 5.0 0.1 1.0

Calcium binding site 4 out of 23 in 6la8

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Calcium binding site 4 out of 23 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca403

b:0.3
occ:1.00
 O2 I:DT315 3.8 0.5 1.0
O4' I:DG316 4.0 0.0 1.0
C5' I:DG316 4.0 0.9 1.0
O4' I:DT315 4.1 0.6 1.0
C4' I:DG316 4.2 0.9 1.0
C4' I:DT315 4.5 0.2 1.0
N2 I:DG314 4.8 0.1 1.0
C4' J:DA33 4.8 0.3 1.0
O2 J:DC32 4.8 0.7 1.0
C1' I:DT315 4.9 0.9 1.0
C2 I:DT315 5.0 0.0 1.0

Calcium binding site 5 out of 23 in 6la8

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Calcium binding site 5 out of 23 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca404

b:0.1
occ:1.00
 O4' I:DA319 3.5 0.1 1.0
N2 I:DG318 3.7 0.8 1.0
C4' I:DA319 3.9 0.6 1.0
O2 J:DT29 3.9 0.1 1.0
N3 I:DG318 4.4 0.8 1.0
C5' I:DA319 4.4 0.9 1.0
C2 I:DG318 4.5 0.3 1.0
O4' J:DC30 4.6 0.9 1.0
C4' J:DC30 4.7 0.4 1.0
C1' I:DA319 4.8 0.4 1.0
N3 I:DA319 4.9 0.9 1.0

Calcium binding site 6 out of 23 in 6la8

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Calcium binding site 6 out of 23 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca405

b:0.7
occ:1.00
 N7 I:DG200 2.7 0.3 1.0
O6 I:DG200 3.3 0.7 1.0
C5 I:DG200 3.5 0.9 1.0
O4 I:DT201 3.6 0.5 1.0
C6 I:DG200 3.7 0.8 1.0
C8 I:DG200 3.8 0.6 1.0
N7 I:DG199 3.9 0.3 1.0
N6 J:DA145 4.2 0.9 1.0
C8 I:DG199 4.2 0.1 1.0
C7 I:DT201 4.3 0.4 1.0
C4 I:DT201 4.5 0.8 1.0
C5 I:DG199 4.5 0.7 1.0
C4 I:DG200 4.7 0.5 1.0
N9 I:DG200 4.9 0.6 1.0
C5 I:DT201 4.9 0.5 1.0
N9 I:DG199 5.0 0.8 1.0

Calcium binding site 7 out of 23 in 6la8

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Calcium binding site 7 out of 23 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca406

b:0.9
occ:1.00
 O6 I:DG308 3.0 0.9 1.0
N7 I:DG308 3.5 0.7 1.0
C6 I:DG308 3.8 0.1 1.0
O6 J:DG37 4.0 1.0 1.0
C5 I:DG308 4.0 0.3 1.0
N7 I:DG307 4.4 0.7 1.0
C8 I:DG307 4.6 0.2 1.0
C8 I:DG308 4.7 0.5 1.0

Calcium binding site 8 out of 23 in 6la8

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Calcium binding site 8 out of 23 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca407

b:0.6
occ:1.00
 N2 I:DG28 3.6 0.5 1.0
O4' J:DA319 3.9 0.8 1.0
O2 I:DC29 4.2 0.7 1.0
O2 J:DC318 4.2 0.7 1.0
C5' I:DC30 4.3 0.0 1.0
N3 J:DA319 4.5 0.5 1.0
C4' J:DA319 4.5 0.6 1.0
C1' J:DA319 4.5 0.6 1.0
O4' I:DC30 4.6 0.3 1.0
C4' I:DC30 4.6 0.4 1.0
O4' I:DC29 4.7 0.2 1.0
C1' I:DC29 4.9 0.1 1.0
C2 I:DG28 4.9 0.9 1.0
C2 I:DC29 4.9 0.4 1.0
C4 J:DA319 5.0 0.4 1.0

Calcium binding site 9 out of 23 in 6la8

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Calcium binding site 9 out of 23 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca408

b:0.2
occ:1.00
 N7 I:DG323 2.6 0.5 1.0
C5 I:DG323 3.5 0.7 1.0
O6 I:DG323 3.5 0.4 1.0
C8 I:DG323 3.6 0.6 1.0
C8 I:DG322 3.7 0.0 1.0
N7 I:DG322 3.7 0.0 1.0
C6 I:DG323 3.9 0.1 1.0
O6 J:DG22 3.9 0.4 1.0
N4 I:DC324 4.1 0.8 1.0
N9 I:DG322 4.4 0.9 1.0
C5 I:DG322 4.5 0.2 1.0
C4 I:DG323 4.7 0.8 1.0
N9 I:DG323 4.7 0.1 1.0
C4 I:DG322 4.9 0.5 1.0
C2' I:DG322 4.9 0.4 1.0

Calcium binding site 10 out of 23 in 6la8

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Calcium binding site 10 out of 23 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca409

b:0.2
occ:1.00
 O6 I:DG2 3.1 0.2 1.0
C5 I:DC1 3.4 0.0 1.0
O6 J:DG343 3.5 0.8 1.0
C6 I:DC1 4.0 0.0 1.0
C4 I:DC1 4.0 0.3 1.0
C6 I:DG2 4.2 0.7 1.0
N4 I:DC1 4.2 0.4 1.0
N7 I:DG2 4.4 0.5 1.0
C6 J:DG343 4.6 0.3 1.0
C5 I:DG2 4.7 0.9 1.0
OP1 I:DC1 4.8 0.0 1.0
N7 J:DG343 4.8 0.2 1.0
N1 I:DC1 4.9 0.3 1.0
N3 I:DC1 4.9 1.0 1.0

Reference:

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
Page generated: Wed Jul 9 15:44:35 2025

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