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Potassium 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:

Calcium (Ca) 23 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 7 binding sites of Potassium where determined in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0, PDB code: 6la8:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 6la8

Go back to Potassium Binding Sites List in 6la8
Potassium binding site 1 out of 7 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 Potassium with other atoms in the K 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
I:K412

b:0.5
occ:1.00
 O2 I:DT234 3.1 0.2 1.0
O4' I:DA235 3.6 0.3 1.0
O4' J:DA114 3.7 0.7 1.0
C4' I:DA235 3.7 0.2 1.0
C4' J:DA114 4.1 0.8 1.0
C2 I:DT234 4.3 0.4 1.0
C5' I:DA235 4.3 0.9 1.0
C5' I:DG236 4.4 0.5 1.0
C5' J:DA114 4.6 0.1 1.0
C1' I:DA235 4.7 0.1 1.0
C2 J:DA112 4.7 0.8 1.0
O4' I:DG236 4.8 0.0 1.0
C1' I:DT234 4.8 0.3 1.0
C1' J:DA114 4.8 0.1 1.0
N3 I:DA235 4.9 0.3 1.0
OP1 I:DG236 5.0 0.2 1.0
N2 J:DG113 5.0 0.7 1.0

Potassium binding site 2 out of 7 in 6la8

Go back to Potassium Binding Sites List in 6la8
Potassium binding site 2 out of 7 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 Potassium with other atoms in the K 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:K413

b:0.9
occ:1.00
 O2 I:DT60 2.9 0.0 1.0
O4' J:DA288 3.5 0.1 1.0
O4' I:DA61 3.9 0.7 1.0
C4' I:DA61 4.0 0.8 1.0
C2 I:DT60 4.1 0.9 1.0
C4' J:DA288 4.2 0.2 1.0
C1' I:DA61 4.2 0.4 1.0
N2 J:DG287 4.4 0.7 1.0
N3 J:DG287 4.5 0.3 1.0
C2 J:DA286 4.5 0.8 1.0
C1' J:DA288 4.5 0.1 1.0
N3 J:DA288 4.7 0.2 1.0
O3' I:DA61 4.8 0.6 1.0
C5' J:DA288 4.8 0.2 1.0
C5' I:DA61 4.8 0.4 1.0
N3 I:DA61 4.9 0.8 1.0
C1' I:DT60 4.9 0.4 1.0
C2 J:DG287 4.9 0.3 1.0
C3' I:DA61 5.0 0.8 1.0
N3 I:DT60 5.0 0.5 1.0
N3 J:DA286 5.0 0.6 1.0

Potassium binding site 3 out of 7 in 6la8

Go back to Potassium Binding Sites List in 6la8
Potassium binding site 3 out of 7 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 Potassium with other atoms in the K 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
J:K411

b:0.8
occ:1.00
 O4' J:DG227 4.0 0.5 1.0
O4' J:DA226 4.1 0.4 1.0
N3 J:DA226 4.2 0.3 1.0
C2 J:DA225 4.4 0.6 1.0
N3 J:DA225 4.5 0.4 1.0
C5' I:DC123 4.5 0.0 1.0
C4' J:DA226 4.5 0.9 1.0
C4' J:DG227 4.6 0.4 1.0
N3 I:DA122 4.6 0.8 1.0
C1' J:DA226 4.7 0.7 1.0
C5' J:DG227 4.7 0.9 1.0
C2 J:DA226 4.9 0.8 1.0
O3' J:DA226 5.0 0.3 1.0

Potassium binding site 4 out of 7 in 6la8

Go back to Potassium Binding Sites List in 6la8
Potassium binding site 4 out of 7 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 Potassium with other atoms in the K 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
J:K412

b:1.0
occ:1.00
 O4' J:DA122 3.9 0.3 1.0
C5' J:DC123 4.2 1.0 1.0
C4' J:DA122 4.4 0.2 1.0
O3' J:DA122 4.5 0.2 1.0
C5' I:DA227 4.5 0.9 1.0
C4' I:DA227 4.5 1.0 1.0
C1' J:DA122 4.5 0.4 1.0
O4' I:DA227 4.6 0.9 1.0
N3 J:DA122 4.6 0.3 1.0
C4' J:DC123 4.9 0.6 1.0
O4' J:DC123 4.9 0.9 1.0

Potassium binding site 5 out of 7 in 6la8

Go back to Potassium Binding Sites List in 6la8
Potassium binding site 5 out of 7 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 Potassium with other atoms in the K 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
J:K413

b:0.2
occ:1.00
 O2 J:DT60 3.2 0.1 1.0
O4' I:DA288 3.5 0.4 1.0
C1' J:DA61 4.1 0.5 1.0
C4' I:DA288 4.1 0.9 1.0
O4' J:DA61 4.3 0.3 1.0
C5' J:DG62 4.4 0.1 1.0
C2 J:DT60 4.4 0.8 1.0
C4' J:DA61 4.4 0.4 1.0
N2 I:DG287 4.5 0.1 1.0
C5' I:DA288 4.6 0.5 1.0
N3 J:DA61 4.6 0.6 1.0
N3 I:DG287 4.7 0.3 1.0
C1' I:DA288 4.7 0.2 1.0
C2 I:DA286 4.7 0.3 1.0
O3' J:DA61 4.7 0.7 1.0
N3 I:DA288 4.8 0.2 1.0
N9 J:DA61 4.9 0.7 1.0
O4' J:DG62 4.9 0.3 1.0
C1' J:DT60 5.0 0.3 1.0

Potassium binding site 6 out of 7 in 6la8

Go back to Potassium Binding Sites List in 6la8
Potassium binding site 6 out of 7 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 Potassium with other atoms in the K 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
J:K414

b:0.4
occ:1.00
 O2 J:DT234 2.9 1.0 1.0
O4' J:DA235 3.2 0.7 1.0
C4' J:DA235 3.7 0.0 1.0
C2 J:DT234 4.0 0.2 1.0
N3 J:DA235 4.1 1.0 1.0
C1' J:DA235 4.1 0.2 1.0
C2 I:DA112 4.2 0.7 1.0
O4' I:DA114 4.3 0.1 1.0
C5' J:DA235 4.3 0.1 1.0
O4' J:DG236 4.4 0.3 1.0
C5' J:DG236 4.6 0.4 1.0
C4 J:DA235 4.6 0.6 1.0
N9 J:DA235 4.6 0.5 1.0
C1' J:DT234 4.7 0.8 1.0
C4' I:DA114 4.7 0.4 1.0
N3 I:DA112 4.8 0.0 1.0
N2 I:DG113 4.8 0.4 1.0
N3 J:DT234 4.9 0.4 1.0
N1 J:DT234 4.9 0.9 1.0
C2 J:DA235 4.9 0.1 1.0
C3' J:DA235 4.9 0.1 1.0
C4' J:DG236 4.9 1.0 1.0

Potassium binding site 7 out of 7 in 6la8

Go back to Potassium Binding Sites List in 6la8
Potassium binding site 7 out of 7 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 Potassium with other atoms in the K 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
J:K415

b:0.9
occ:1.00
 O4' J:DG53 3.9 0.1 1.0
N3 J:DA52 3.9 0.3 1.0
O4' J:DA52 3.9 0.5 1.0
C2 J:DA51 4.1 0.8 1.0
N3 J:DA51 4.1 0.1 1.0
C5' J:DG53 4.3 0.6 1.0
C4' J:DG53 4.4 0.6 1.0
N3 I:DA296 4.4 0.7 1.0
C2 J:DA52 4.5 0.1 1.0
O2 I:DT295 4.5 1.0 1.0
C4' J:DA52 4.6 0.2 1.0
C1' J:DA52 4.8 0.3 1.0
C2 I:DA296 4.8 0.5 1.0
C4 J:DA52 4.9 0.3 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: Mon Aug 12 16:47:41 2024

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