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Potassium in PDB 6l9z: 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X

Protein crystallography data

The structure of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X, PDB code: 6l9z 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) 213.83 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.5, 101.41, 215.67, 90, 97.48, 90
R / Rfree (%) 20.4 / 25.6

Other elements in 6l9z:

The structure of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Calcium (Ca) 65 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X (pdb code 6l9z). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X, PDB code: 6l9z:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 6l9z

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Potassium binding site 1 out of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K205

b:93.7
occ:1.00
O G:ASN38 2.7 60.0 1.0
O C:ASN38 2.8 77.1 1.0
C G:ASN38 3.9 58.0 1.0
C C:ASN38 4.0 66.7 1.0
OG H:SER78 4.2 54.1 1.0
CB C:ASN38 4.5 73.1 1.0
CB G:ASN38 4.6 70.7 1.0
CA G:TYR39 4.6 53.7 1.0
CD1 G:TYR39 4.7 46.3 1.0
CA C:TYR39 4.7 59.4 1.0
N G:TYR39 4.7 53.0 1.0
N C:TYR39 4.8 62.6 1.0
OG D:SER78 4.8 54.4 1.0
CA G:ASN38 4.9 63.8 1.0
O C:GLY37 4.9 62.0 1.0
CA C:ASN38 4.9 70.5 1.0
CD1 C:TYR39 5.0 50.0 1.0
O G:GLY37 5.0 58.8 1.0

Potassium binding site 2 out of 10 in 6l9z

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Potassium binding site 2 out of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K429

b:80.5
occ:1.00
O J:HOH529 2.4 64.2 1.0
O2 I:DT228 2.4 74.1 1.0
O I:HOH525 2.7 48.1 1.0
O J:HOH538 2.8 31.7 1.0
O4' I:DA229 3.1 69.1 1.0
C2 I:DT228 3.6 70.7 1.0
C4' I:DA229 3.6 65.2 1.0
O4' J:DA113 3.9 70.0 1.0
C5' I:DA229 4.0 64.2 1.0
O I:HOH514 4.1 47.3 1.0
C1' I:DA229 4.2 69.9 1.0
C1' I:DT228 4.3 66.0 1.0
N1 I:DT228 4.4 71.3 1.0
N2 J:DG112 4.4 87.0 1.0
C4' J:DA113 4.5 63.1 1.0
N3 I:DT228 4.5 75.8 1.0
O P:HOH208 4.6 40.1 1.0
C2 J:DA111 4.6 63.3 1.0
N3 I:DA229 4.7 70.6 1.0
N9 I:DA229 4.8 71.6 1.0
N3 J:DG112 4.9 85.7 1.0
C3' I:DA229 4.9 63.3 1.0
C5' J:DA113 5.0 59.2 1.0

Potassium binding site 3 out of 10 in 6l9z

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Potassium binding site 3 out of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K430

b:80.7
occ:1.00
O I:HOH534 2.7 55.5 1.0
O2 I:DT59 2.7 61.5 1.0
O4' J:DA282 3.5 66.5 1.0
O4' I:DA60 3.7 67.8 1.0
C2 I:DT59 4.0 67.9 1.0
C4' I:DA60 4.0 62.2 1.0
C4' J:DA282 4.0 61.6 1.0
N2 J:DG281 4.4 79.0 1.0
C1' J:DA282 4.5 70.9 1.0
C5' I:DA60 4.5 58.0 1.0
C1' I:DT59 4.6 66.9 1.0
C1' I:DA60 4.7 70.3 1.0
N1 I:DT59 4.8 70.3 1.0
C5' J:DA282 4.8 61.7 1.0
N3 J:DG281 4.9 80.6 1.0
C2 J:DA280 4.9 68.8 1.0
N3 I:DT59 4.9 76.5 1.0
N3 J:DA282 5.0 73.0 1.0

Potassium binding site 4 out of 10 in 6l9z

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Potassium binding site 4 out of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K431

b:97.9
occ:1.00
O I:HOH505 2.1 79.1 1.0
O J:HOH521 2.4 64.2 1.0
O I:HOH542 2.4 65.3 1.0
O I:HOH501 2.8 70.5 1.0
N3 I:DA219 4.1 87.8 1.0
O4' I:DG220 4.2 80.4 1.0
C2 I:DA219 4.2 85.1 1.0
N3 I:DG220 4.3 90.4 1.0
N2 I:DG220 4.5 89.5 1.0
C4' I:DG220 4.5 71.8 1.0
N3 J:DA121 4.6 87.6 1.0
O4' I:DA221 4.7 88.8 1.0
O2 J:DT120 4.7 96.8 1.0
O4' J:DA121 4.7 87.5 1.0
C2 I:DG220 4.8 88.2 1.0
C1' I:DG220 4.9 83.1 1.0
O4' J:DC122 4.9 82.6 1.0

Potassium binding site 5 out of 10 in 6l9z

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Potassium binding site 5 out of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K432

b:100.0
occ:1.00
O J:HOH523 2.4 84.2 1.0
O J:HOH515 2.5 73.4 1.0
O I:HOH507 2.6 69.2 1.0
O I:HOH543 2.9 78.9 1.0
O4' I:DA121 4.2 108.7 1.0
C2 J:DA219 4.5 86.3 1.0
N3 I:DA121 4.5 104.1 1.0
C4' I:DA121 4.6 117.7 1.0
O4' J:DA220 4.7 84.9 1.0
O4' I:DC122 4.7 92.8 1.0
O2 I:DT120 4.7 114.7 1.0
N3 J:DA219 4.8 89.6 1.0
O4' J:DG221 4.8 94.2 1.0
C1' I:DA121 4.8 102.2 1.0
C4' J:DA220 5.0 78.6 1.0
N3 J:DA220 5.0 91.9 1.0
O3' I:DA121 5.0 113.1 1.0

Potassium binding site 6 out of 10 in 6l9z

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Potassium binding site 6 out of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K433

b:115.0
occ:1.00
O I:HOH535 3.0 64.5 1.0
O2 I:DT289 3.8 84.9 1.0
O4' I:DA290 4.0 78.6 1.0
O4' J:DG52 4.1 79.9 1.0
N3 J:DA51 4.3 77.6 1.0
C4' I:DA290 4.4 82.2 1.0
C2 J:DA51 4.5 72.0 1.0
C4' J:DG52 4.5 86.7 1.0
C1' I:DA290 4.9 82.7 1.0
C2 I:DT289 4.9 95.6 1.0

Potassium binding site 7 out of 10 in 6l9z

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Potassium binding site 7 out of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K434

b:110.2
occ:1.00
O4' J:DA290 4.1 91.2 1.0
N3 J:DA290 4.5 95.7 1.0
O4' I:DA52 4.5 96.4 1.0
C4' J:DA290 4.7 88.3 1.0
C1' J:DA290 4.7 86.5 1.0
O2 J:DT289 4.7 86.4 1.0
N2 I:DG51 4.7 91.4 1.0
C5' I:DA52 4.8 89.5 1.0
C5' J:DC291 4.8 82.7 1.0
N3 I:DG51 4.8 85.7 1.0
C4' I:DA52 4.8 94.2 1.0
O4' I:DG51 4.8 84.3 1.0
C2 I:DA50 4.9 76.3 1.0
O4' J:DC291 5.0 85.4 1.0

Potassium binding site 8 out of 10 in 6l9z

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Potassium binding site 8 out of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K424

b:77.5
occ:1.00
O I:HOH513 2.5 50.9 1.0
O J:HOH513 2.6 45.5 1.0
O J:HOH531 2.6 50.4 1.0
O2 J:DT59 2.8 75.3 1.0
O4' J:DA60 3.4 57.1 1.0
O L:HOH210 3.4 43.8 1.0
C4' J:DA60 3.8 52.4 1.0
O4' I:DA282 3.9 60.9 1.0
C2 J:DT59 4.0 68.9 1.0
C1' J:DA60 4.3 60.9 1.0
C4' I:DA282 4.3 55.1 1.0
C2 I:DA280 4.4 59.0 1.0
N3 J:DA60 4.4 66.1 1.0
N2 I:DG281 4.5 69.7 1.0
C5' J:DA60 4.5 52.2 1.0
C1' J:DT59 4.8 61.5 1.0
N3 I:DG281 4.8 65.0 1.0
N9 J:DA60 4.8 66.4 1.0
O4' J:DG61 4.8 54.5 1.0
N3 J:DT59 4.9 67.5 1.0
N1 J:DT59 4.9 61.5 1.0
C4 J:DA60 4.9 66.4 1.0
C5' I:DA282 4.9 54.8 1.0
C1' I:DA282 4.9 58.6 1.0
N1 I:DA280 5.0 67.0 1.0

Potassium binding site 9 out of 10 in 6l9z

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Potassium binding site 9 out of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K425

b:77.5
occ:1.00
O J:HOH509 2.6 56.5 1.0
O J:HOH516 2.6 54.3 1.0
O2 J:DT228 2.6 92.3 1.0
O4' J:DA229 3.4 76.9 1.0
C2 J:DT228 3.8 86.2 1.0
C4' J:DA229 3.9 73.4 1.0
O4' I:DA113 3.9 70.1 1.0
C2 I:DA111 4.3 66.3 1.0
O I:HOH523 4.3 61.6 1.0
N3 J:DA229 4.4 89.8 1.0
C1' J:DA229 4.4 80.2 1.0
C4' I:DA113 4.5 66.9 1.0
C5' J:DA229 4.5 71.2 1.0
N3 J:DT228 4.6 89.4 1.0
N2 I:DG112 4.6 89.2 1.0
C1' J:DT228 4.7 74.1 1.0
N1 J:DT228 4.7 77.6 1.0
N1 I:DA111 4.8 73.8 1.0
O4' J:DG230 4.9 54.4 1.0
N3 I:DG112 4.9 88.2 1.0
C1' I:DA113 4.9 72.6 1.0
C4 J:DA229 4.9 91.4 1.0
N9 J:DA229 4.9 88.7 1.0

Potassium binding site 10 out of 10 in 6l9z

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Potassium binding site 10 out of 10 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X within 5.0Å range:
probe atom residue distance (Å) B Occ
M:K204

b:80.6
occ:1.00
O Q:HOH304 2.6 55.4 1.0
O M:ASN38 2.7 65.2 1.0
O Q:ASN38 2.8 49.3 1.0
O N:HOH306 3.1 44.9 1.0
C M:ASN38 3.9 57.7 1.0
C Q:ASN38 4.0 47.8 1.0
OG R:SER78 4.3 51.6 1.0
CB M:ASN38 4.4 69.2 1.0
CB Q:ASN38 4.6 62.7 1.0
O M:GLY37 4.6 68.9 1.0
CA Q:TYR39 4.7 47.2 1.0
CA M:TYR39 4.8 49.9 1.0
N Q:TYR39 4.8 50.0 1.0
N M:TYR39 4.8 53.4 1.0
CA M:ASN38 4.8 61.9 1.0
CD1 M:TYR39 4.8 39.7 1.0
OG N:SER78 4.8 51.0 1.0
CD1 Q:TYR39 4.9 42.6 1.0
CA Q:ASN38 4.9 54.3 1.0

Reference:

D.Sharma, C.A.Davey, Z.Adhireksan. Dinucleosome 338 Bp with Linker Histone H1.X To Be Published.
Page generated: Wed Mar 3 14:15:18 2021

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