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Chlorine 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:

Potassium (K) 10 atoms
Calcium (Ca) 65 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 8 binding sites of Chlorine where determined in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X, PDB code: 6l9z:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6l9z

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Chlorine binding site 1 out of 8 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
A:Cl201

b:72.7
occ:1.00
 N A:LYS122 3.1 52.9 1.0
CD A:PRO121 3.4 57.6 1.0
N A:PRO121 3.5 55.2 1.0
CB A:PRO121 3.7 56.1 1.0
CB A:MET120 3.7 58.4 1.0
CB A:LYS122 3.7 53.7 1.0
CG A:LYS122 3.8 58.2 1.0
CD A:LYS122 3.8 62.6 1.0
CG A:PRO121 3.9 57.7 1.0
CA A:PRO121 3.9 55.9 1.0
C A:PRO121 4.0 56.4 1.0
CA A:LYS122 4.0 54.0 1.0
C A:MET120 4.2 53.3 1.0
CA A:MET120 4.5 53.3 1.0
SD A:MET120 4.6 67.1 1.0
CG A:MET120 4.7 61.6 1.0
O A:MET120 5.0 53.2 1.0

Chlorine binding site 2 out of 8 in 6l9z

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Chlorine binding site 2 out of 8 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
C:Cl204

b:55.1
occ:1.00
 N C:GLY46 3.2 50.2 1.0
N D:SER91 3.3 54.3 1.0
CA D:THR90 3.6 49.2 1.0
C C:GLY44 3.6 53.7 1.0
N C:ALA45 3.6 56.3 1.0
CB D:THR90 3.6 49.1 1.0
CA C:GLY46 3.7 52.4 1.0
CA C:GLY44 3.7 54.1 1.0
N C:ALA47 3.8 51.7 1.0
C D:THR90 3.9 50.0 1.0
OG D:SER91 4.1 54.0 1.0
C C:GLY46 4.1 54.0 1.0
O C:GLY44 4.1 55.7 1.0
OP1 J:DG292 4.2 74.7 1.0
C C:ALA45 4.2 52.4 1.0
CB D:SER91 4.3 51.6 1.0
CG2 D:THR90 4.4 45.0 1.0
CA D:SER91 4.4 53.9 1.0
CA C:ALA45 4.4 55.3 1.0
OG1 D:THR90 4.8 48.6 1.0
CA C:ALA47 4.8 50.1 1.0
N C:GLY44 4.8 55.1 1.0
CB C:ALA47 4.9 52.9 1.0
N D:THR90 4.9 47.6 1.0

Chlorine binding site 3 out of 8 in 6l9z

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Chlorine binding site 3 out of 8 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
E:Cl201

b:66.5
occ:1.00
 N E:LYS122 3.2 43.6 1.0
CD E:PRO121 3.4 58.4 1.0
N E:PRO121 3.6 54.3 1.0
CB E:LYS122 3.7 46.9 1.0
CG E:LYS122 3.8 51.8 1.0
CB E:PRO121 3.8 53.7 1.0
CG E:PRO121 3.9 57.9 1.0
CB E:MET120 4.0 53.7 1.0
CA E:LYS122 4.0 46.7 1.0
CA E:PRO121 4.0 54.5 1.0
C E:PRO121 4.1 49.7 1.0
CD E:LYS122 4.1 58.3 1.0
C E:MET120 4.4 50.9 1.0
CE E:LYS122 4.5 65.8 1.0
CA E:MET120 4.7 52.1 1.0
SD E:MET120 4.9 62.9 1.0
CD1 F:LEU49 5.0 50.2 1.0

Chlorine binding site 4 out of 8 in 6l9z

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Chlorine binding site 4 out of 8 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
G:Cl204

b:61.0
occ:1.00
 N G:GLY46 3.1 56.7 1.0
N H:SER91 3.2 49.3 1.0
C G:GLY44 3.5 57.8 1.0
N G:ALA47 3.5 51.8 1.0
CA G:GLY46 3.5 58.2 1.0
CA H:THR90 3.6 53.2 1.0
CA G:GLY44 3.6 58.5 1.0
N G:ALA45 3.6 56.7 1.0
CB H:THR90 3.7 52.9 1.0
C H:THR90 3.8 51.2 1.0
O G:GLY44 3.9 58.8 1.0
C G:GLY46 3.9 54.6 1.0
OG H:SER91 4.0 60.7 1.0
C G:ALA45 4.2 58.7 1.0
CB H:SER91 4.2 54.8 1.0
OP1 I:DT123 4.2 98.3 1.0
CA H:SER91 4.3 51.6 1.0
CA G:ALA45 4.5 57.7 1.0
CA G:ALA47 4.5 51.7 1.0
CG2 H:THR90 4.5 50.6 1.0
CB G:ALA47 4.6 56.7 1.0
N G:GLY44 4.6 58.6 1.0
O H:ILE89 4.8 55.3 1.0
OG1 H:THR90 4.8 56.0 1.0
N H:THR90 4.9 53.7 1.0

Chlorine binding site 5 out of 8 in 6l9z

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Chlorine binding site 5 out of 8 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
K:Cl201

b:64.6
occ:1.00
 N K:LYS122 3.2 40.0 1.0
CG K:LYS122 3.6 47.5 1.0
CB K:LYS122 3.6 42.3 1.0
CD K:PRO121 3.6 50.4 1.0
CE K:LYS122 3.7 63.1 1.0
N K:PRO121 3.7 49.6 1.0
CB K:MET120 3.8 48.6 1.0
CB K:PRO121 3.9 48.1 1.0
CD K:LYS122 4.0 53.9 1.0
CA K:LYS122 4.0 41.3 1.0
C K:PRO121 4.1 44.7 1.0
CA K:PRO121 4.1 47.8 1.0
CG K:PRO121 4.2 46.7 1.0
C K:MET120 4.4 44.1 1.0
SD K:MET120 4.5 57.6 1.0
CA K:MET120 4.7 46.0 1.0
CG K:MET120 4.7 52.3 1.0
NZ K:LYS122 4.9 75.6 1.0

Chlorine binding site 6 out of 8 in 6l9z

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Chlorine binding site 6 out of 8 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
M:Cl203

b:48.3
occ:1.00
 N M:GLY46 3.2 45.3 1.0
N N:SER91 3.4 42.3 1.0
CA M:GLY46 3.5 48.1 1.0
C M:GLY44 3.6 47.0 1.0
CA N:THR90 3.6 43.1 1.0
CB N:THR90 3.6 44.2 1.0
CA M:GLY44 3.7 47.6 1.0
N M:ALA47 3.7 46.9 1.0
N M:ALA45 3.8 51.3 1.0
C N:THR90 4.0 43.1 1.0
C M:GLY46 4.1 51.1 1.0
O M:GLY44 4.1 45.9 1.0
OG N:SER91 4.2 48.1 1.0
CG2 N:THR90 4.2 41.1 1.0
C M:ALA45 4.3 46.7 1.0
CB N:SER91 4.3 42.7 1.0
OP1 I:DT292 4.3 65.6 1.0
CA N:SER91 4.4 42.0 1.0
CA M:ALA45 4.6 48.7 1.0
CA M:ALA47 4.7 40.6 1.0
N M:GLY44 4.7 49.3 1.0
CB M:ALA47 4.8 41.6 1.0
OG1 N:THR90 4.8 44.8 1.0
N N:THR90 4.9 44.1 1.0
O N:ILE89 5.0 52.2 1.0

Chlorine binding site 7 out of 8 in 6l9z

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Chlorine binding site 7 out of 8 in the 338 Bp Di-Nucleosome Assembled with Linker Histone H1.X


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
O:Cl201

b:49.5
occ:1.00
 N O:LYS122 3.3 40.3 1.0
CG O:LYS122 3.6 51.7 1.0
CD O:PRO121 3.6 43.0 1.0
N O:PRO121 3.7 40.3 1.0
CB O:LYS122 3.7 44.2 1.0
CB O:PRO121 3.8 40.8 1.0
CB O:MET120 3.8 43.0 1.0
CG O:PRO121 4.0 43.4 1.0
CD O:LYS122 4.0 59.3 1.0
CA O:PRO121 4.1 40.6 1.0
CA O:LYS122 4.1 40.2 1.0
C O:PRO121 4.1 39.4 1.0
CE O:LYS122 4.2 66.3 1.0
C O:MET120 4.4 42.2 1.0
CA O:MET120 4.7 41.1 1.0
SD O:MET120 4.7 47.1 1.0
CG O:MET120 4.8 44.3 1.0
NZ O:LYS122 4.9 70.0 1.0

Chlorine binding site 8 out of 8 in 6l9z

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
Q:Cl203

b:51.1
occ:1.00
 N Q:GLY46 3.1 53.0 1.0
N R:SER91 3.3 50.7 1.0
CA Q:GLY46 3.5 57.5 1.0
N Q:ALA47 3.5 57.4 1.0
CA R:THR90 3.6 45.8 1.0
CB R:THR90 3.6 49.9 1.0
C Q:GLY44 3.6 54.9 1.0
CA Q:GLY44 3.7 50.9 1.0
N Q:ALA45 3.7 56.6 1.0
OG R:SER91 3.8 62.7 1.0
C R:THR90 3.9 49.0 1.0
C Q:GLY46 3.9 61.0 1.0
O Q:GLY44 4.0 58.6 1.0
CB R:SER91 4.2 51.6 1.0
C Q:ALA45 4.2 53.3 1.0
OP1 J:DG123 4.3 78.5 1.0
CA R:SER91 4.3 48.1 1.0
CG2 R:THR90 4.4 50.2 1.0
CA Q:ALA47 4.5 52.8 1.0
CA Q:ALA45 4.5 54.2 1.0
OG1 R:THR90 4.6 43.9 1.0
CB Q:ALA47 4.6 55.0 1.0
N Q:GLY44 4.6 49.5 1.0
N R:THR90 4.9 42.9 1.0
O R:ILE89 4.9 46.1 1.0

Reference:

D.Sharma, C.A.Davey, Z.Adhireksan. Dinucleosome 338 Bp with Linker Histone H1.X To Be Published.
Page generated: Sat Jul 12 16:27:57 2025

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