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Calcium in PDB 6la9: 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)

Protein crystallography data

The structure of 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant), PDB code: 6la9 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) 91.78 / 3.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.780, 172.880, 216.041, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 26.6

Other elements in 6la9:

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

Potassium (K) 2 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Calcium atom in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant) (pdb code 6la9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 40 binding sites of Calcium where determined in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant), PDB code: 6la9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 40 in 6la9

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Calcium binding site 1 out of 40 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:0.7
occ:1.00
 O A:ASP77 3.0 0.9 1.0
C A:ASP77 4.1 0.9 1.0
CA A:ASP77 4.4 0.5 1.0

Calcium binding site 2 out of 40 in 6la9

Go back to Calcium Binding Sites List in 6la9
Calcium binding site 2 out of 40 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:0.4
occ:1.00
 O C:HOH301 3.6 66.9 1.0
OE2 C:GLU41 4.1 0.6 1.0
OE1 C:GLU41 4.4 0.9 1.0
CA J:CA401 4.5 0.8 1.0
CD C:GLU41 4.5 0.4 1.0
CA G:CA201 4.6 0.1 1.0
CB G:GLU41 4.9 0.7 1.0
CA G:GLU41 4.9 0.8 1.0

Calcium binding site 3 out of 40 in 6la9

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Calcium binding site 3 out of 40 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:0.1
occ:1.00
 OD2 F:ASP24 3.7 0.3 1.0
OD1 F:ASP24 3.9 0.1 1.0
CG F:ASP24 4.1 0.4 1.0
CB F:ARG23 4.9 0.9 1.0

Calcium binding site 4 out of 40 in 6la9

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Calcium binding site 4 out of 40 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:0.1
occ:1.00
 OE2 G:GLU41 2.6 0.4 1.0
CD G:GLU41 3.0 0.8 1.0
OE1 G:GLU41 3.5 0.4 1.0
CG G:GLU41 3.8 0.1 1.0
CB G:GLU41 4.3 0.7 1.0
CA C:CA201 4.6 0.4 1.0
CA J:CA401 4.9 0.8 1.0

Calcium binding site 5 out of 40 in 6la9

Go back to Calcium Binding Sites List in 6la9
Calcium binding site 5 out of 40 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca202

b:0.8
occ:1.00
 O H:VAL48 2.4 0.8 1.0
OE1 G:GLU64 2.5 0.2 1.0
CD G:GLU64 3.2 0.2 1.0
OE2 G:GLU64 3.2 0.1 1.0
CE1 H:HIS49 3.4 0.9 1.0
C H:VAL48 3.6 0.2 1.0
ND1 H:HIS49 3.7 0.4 1.0
NE2 H:HIS49 3.9 0.9 1.0
CA H:VAL48 4.2 0.8 1.0
CG H:HIS49 4.3 0.3 1.0
CD2 H:HIS49 4.5 0.5 1.0
CB H:VAL48 4.6 0.3 1.0
N H:HIS49 4.6 0.7 1.0
CG G:GLU64 4.7 0.8 1.0
CA H:HIS49 5.0 0.4 1.0

Calcium binding site 6 out of 40 in 6la9

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Calcium binding site 6 out of 40 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca401

b:0.1
occ:1.00
 O4' I:DG316 3.6 0.2 1.0
O2 I:DT315 3.7 0.3 1.0
C4' I:DG316 4.0 0.3 1.0
O2 J:DC32 4.2 0.3 1.0
O4' J:DA33 4.2 0.1 1.0
C4' J:DA33 4.3 0.4 1.0
N2 I:DG314 4.3 0.9 1.0
NH2 Q:ARG77 4.3 0.6 1.0
O4' I:DT315 4.4 0.9 1.0
C5' I:DG316 4.4 0.6 1.0
C5' J:DA33 4.5 0.2 1.0
C2 I:DT315 4.9 0.7 1.0
C1' I:DG316 4.9 0.3 1.0
C1' I:DT315 4.9 0.2 1.0

Calcium binding site 7 out of 40 in 6la9

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Calcium binding site 7 out of 40 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca402

b:0.5
occ:1.00
 O6 I:DG34 3.1 0.5 1.0
O6 J:DG311 3.3 0.2 1.0
N4 I:DC35 3.5 0.3 1.0
N7 I:DG34 3.6 0.9 1.0
C6 I:DG34 3.7 0.5 1.0
C5 I:DG34 3.9 0.3 1.0
C6 J:DG311 4.4 0.3 1.0
C4 I:DC35 4.6 0.6 1.0
C8 I:DG34 4.7 0.4 1.0
N1 I:DG34 4.9 0.2 1.0

Calcium binding site 8 out of 40 in 6la9

Go back to Calcium Binding Sites List in 6la9
Calcium binding site 8 out of 40 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca403

b:0.8
occ:1.00
 O2 I:DC203 3.6 0.2 1.0
O4' I:DC203 3.8 0.1 1.0
C5' I:DC204 3.8 0.6 1.0
O4' I:DC204 3.9 0.6 1.0
C4' I:DC204 4.0 0.7 1.0
N2 I:DG202 4.1 0.8 1.0
O4' J:DA145 4.3 0.1 1.0
C1' I:DC203 4.6 0.3 1.0
C2 I:DC203 4.6 0.8 1.0
C4' J:DA145 4.6 1.0 1.0
O2 J:DC144 4.7 0.9 1.0
C4' I:DC203 4.7 0.9 1.0

Calcium binding site 9 out of 40 in 6la9

Go back to Calcium Binding Sites List in 6la9
Calcium binding site 9 out of 40 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca404

b:0.5
occ:1.00
 O6 J:DG134 3.2 1.0 1.0
O6 I:DG211 3.4 0.1 1.0
N7 J:DG134 3.9 0.2 1.0
C6 J:DG134 4.0 0.9 1.0
N4 J:DC135 4.2 0.3 1.0
C5 J:DG134 4.3 0.7 1.0
C6 I:DG211 4.4 0.8 1.0
N4 I:DC210 4.5 0.1 1.0
N7 I:DG211 4.7 0.5 1.0
C4 I:DC210 4.8 0.7 1.0
C5 I:DC210 4.8 0.4 1.0
C5 I:DG211 5.0 0.9 1.0
N4 I:DC212 5.0 0.4 1.0

Calcium binding site 10 out of 40 in 6la9

Go back to Calcium Binding Sites List in 6la9
Calcium binding site 10 out of 40 in the 349 Bp Di-Nucleosome Harboring Cohesive Dna Termini Assembled with Linker Histone H1.0 (High Cryoprotectant)


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 (High Cryoprotectant) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca405

b:0.3
occ:1.00
 O6 I:DG230 4.2 0.3 1.0
O6 J:DG115 4.8 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: Tue Jul 16 10:46:30 2024

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