Chlorine in PDB 8yti: Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)

Protein crystallography data

The structure of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment), PDB code: 8yti was solved by Z.Adhireksan, B.Qiuye, S.Padavattan, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.22 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.852, 102.111, 216.179, 90, 96.34, 90
R / Rfree (%) 21 / 26.7

Other elements in 8yti:

The structure of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) also contains other interesting chemical elements:

Calcium (Ca) 52 atoms
Potassium (K) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) (pdb code 8yti). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment), PDB code: 8yti:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8yti

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Chlorine binding site 1 out of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:99.0
occ:1.00
 N A:LYS122 3.1 69.8 1.0
CD A:PRO121 3.2 89.8 1.0
N A:PRO121 3.5 86.0 1.0
CB A:PRO121 3.5 88.9 1.0
CB A:LYS122 3.6 72.9 1.0
CG A:LYS122 3.6 75.5 1.0
CG A:PRO121 3.6 89.8 1.0
CB A:MET120 3.8 79.5 1.0
CA A:PRO121 3.9 85.6 1.0
C A:PRO121 3.9 81.2 1.0
CA A:LYS122 3.9 70.9 1.0
CD A:LYS122 4.1 79.3 1.0
C A:MET120 4.1 79.6 1.0
CA A:MET120 4.5 75.6 1.0
CG A:MET120 4.9 80.8 1.0
SD A:MET120 4.9 83.1 1.0
O A:MET120 4.9 79.1 1.0

Chlorine binding site 2 out of 8 in 8yti

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Chlorine binding site 2 out of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl204

b:91.4
occ:1.00
 N C:GLY46 2.9 86.2 1.0
CA C:GLY46 3.4 81.6 1.0
CA C:GLY44 3.4 77.4 1.0
N C:ALA45 3.4 89.8 1.0
C C:GLY44 3.4 81.0 1.0
N C:ALA47 3.6 80.9 1.0
N D:SER91 3.6 73.7 1.0
CA D:THR90 3.7 69.7 1.0
CB D:THR90 3.8 72.9 1.0
C C:GLY46 3.9 84.2 1.0
C C:ALA45 4.0 88.8 1.0
OP1 J:DG38 4.0 90.9 1.0
C D:THR90 4.1 75.3 1.0
O C:GLY44 4.1 81.5 1.0
OG D:SER91 4.2 74.0 1.0
CA C:ALA45 4.3 87.5 1.0
CG2 D:THR90 4.3 70.6 1.0
N C:GLY44 4.5 78.1 1.0
CB D:SER91 4.5 74.1 1.0
CA C:ALA47 4.7 77.5 1.0
CA D:SER91 4.7 75.0 1.0
CB C:ALA47 4.7 80.2 1.0
O D:ILE89 4.9 71.3 1.0
N D:THR90 5.0 65.9 1.0

Chlorine binding site 3 out of 8 in 8yti

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Chlorine binding site 3 out of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl201

b:82.2
occ:1.00
 N E:LYS122 3.2 74.4 1.0
CD E:PRO121 3.5 65.9 1.0
CG E:LYS122 3.6 82.9 1.0
CB E:LYS122 3.6 79.2 1.0
N E:PRO121 3.6 66.1 1.0
CB E:PRO121 3.8 69.2 1.0
CB E:MET120 3.9 79.0 1.0
CA E:LYS122 4.0 75.8 1.0
CD E:LYS122 4.0 86.3 1.0
C E:PRO121 4.0 74.8 1.0
CA E:PRO121 4.0 69.6 1.0
CG E:PRO121 4.1 67.4 1.0
C E:MET120 4.2 68.3 1.0
CE E:LYS122 4.4 92.6 1.0
NZ E:LYS122 4.7 94.4 1.0
CA E:MET120 4.7 70.6 1.0
O E:MET120 4.9 71.7 1.0

Chlorine binding site 4 out of 8 in 8yti

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Chlorine binding site 4 out of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl204

b:75.3
occ:1.00
 N G:GLY46 3.0 74.4 1.0
N H:SER91 3.4 73.0 1.0
CA G:GLY46 3.5 76.8 1.0
N G:ALA45 3.5 83.1 1.0
C G:GLY44 3.5 78.6 1.0
CA G:GLY44 3.5 73.1 1.0
CA H:THR90 3.6 71.3 1.0
CB H:THR90 3.7 68.5 1.0
N G:ALA47 3.7 73.5 1.0
C H:THR90 4.0 75.0 1.0
C G:GLY46 4.1 73.7 1.0
OP1 I:DG38 4.1 99.3 1.0
C G:ALA45 4.2 76.7 1.0
O G:GLY44 4.2 70.4 1.0
CG2 H:THR90 4.2 66.4 1.0
OG H:SER91 4.3 77.7 1.0
CB H:SER91 4.3 77.3 1.0
CA H:SER91 4.4 75.1 1.0
CA G:ALA45 4.5 83.1 1.0
N G:GLY44 4.7 75.8 1.0
CA G:ALA47 4.8 75.6 1.0
CB G:ALA47 4.8 79.8 1.0
OG1 H:THR90 4.9 66.5 1.0
N H:THR90 5.0 66.2 1.0

Chlorine binding site 5 out of 8 in 8yti

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Chlorine binding site 5 out of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl201

b:76.7
occ:1.00
 N K:LYS122 3.2 49.7 1.0
CD K:PRO121 3.2 48.1 1.0
N K:PRO121 3.5 47.8 1.0
CB K:PRO121 3.5 47.8 1.0
CG K:PRO121 3.7 47.7 1.0
CB K:MET120 3.8 51.3 1.0
CB K:LYS122 3.8 55.2 1.0
CG K:LYS122 3.8 54.9 1.0
CA K:PRO121 3.9 51.3 1.0
C K:PRO121 4.0 49.8 1.0
CA K:LYS122 4.1 52.3 1.0
C K:MET120 4.1 46.4 1.0
CD K:LYS122 4.3 59.9 1.0
CA K:MET120 4.5 48.4 1.0
CE K:LYS122 4.7 70.0 1.0
SD K:MET120 4.7 59.3 1.0
CG K:MET120 4.8 53.2 1.0
O K:MET120 4.8 50.2 1.0

Chlorine binding site 6 out of 8 in 8yti

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Chlorine binding site 6 out of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl201

b:63.0
occ:1.00
 N M:GLY46 3.2 57.0 1.0
N N:SER91 3.4 58.4 1.0
CA M:GLY46 3.6 57.5 1.0
CB N:THR90 3.7 53.9 1.0
CA N:THR90 3.7 53.1 1.0
C M:GLY44 3.7 56.5 1.0
CA M:GLY44 3.7 56.2 1.0
N M:ALA45 3.8 57.6 1.0
N M:ALA47 3.9 56.7 1.0
OG N:SER91 4.0 62.0 1.0
C N:THR90 4.0 56.1 1.0
C M:GLY46 4.2 59.6 1.0
OP1 T:DG38 4.2 75.2 1.0
CB N:SER91 4.2 59.6 1.0
O M:GLY44 4.2 64.0 1.0
CG2 N:THR90 4.3 53.2 1.0
C M:ALA45 4.4 59.3 1.0
CA N:SER91 4.4 60.1 1.0
CA M:ALA45 4.7 59.8 1.0
N M:GLY44 4.8 58.2 1.0
OG1 N:THR90 4.8 54.1 1.0
CA M:ALA47 4.9 52.3 1.0
CB M:ALA47 4.9 55.0 1.0

Chlorine binding site 7 out of 8 in 8yti

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Chlorine binding site 7 out of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cl201

b:71.5
occ:1.00
 N O:LYS122 3.5 47.9 1.0
CD O:PRO121 3.6 52.2 1.0
CB O:LYS122 3.8 50.0 1.0
N O:PRO121 3.9 52.0 1.0
CG O:LYS122 3.9 52.9 1.0
CB O:PRO121 3.9 52.6 1.0
CB O:MET120 3.9 50.2 1.0
CD O:LYS122 4.1 55.9 1.0
CG O:PRO121 4.1 52.8 1.0
CA O:PRO121 4.3 52.1 1.0
CA O:LYS122 4.3 48.8 1.0
C O:PRO121 4.3 49.9 1.0
CE O:LYS122 4.4 60.0 1.0
C O:MET120 4.5 48.4 1.0
SD O:MET120 4.7 55.3 1.0
CA O:MET120 4.8 49.3 1.0
CG O:MET120 4.8 52.7 1.0
NZ O:LYS122 4.9 63.8 1.0

Chlorine binding site 8 out of 8 in 8yti

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Chlorine binding site 8 out of 8 in the Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Nucleosome-H1X Linker Histone Assembly (Sticky- 169A Dna Fragment) within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl202

b:65.5
occ:1.00
 N Q:GLY46 3.1 59.6 1.0
N R:SER91 3.2 54.9 1.0
CA R:THR90 3.5 55.4 1.0
CB R:THR90 3.5 54.6 1.0
CA Q:GLY46 3.5 61.6 1.0
C Q:GLY44 3.6 60.7 1.0
CA Q:GLY44 3.6 56.8 1.0
N Q:ALA47 3.6 62.5 1.0
N Q:ALA45 3.7 66.4 1.0
C R:THR90 3.8 57.3 1.0
OG R:SER91 4.0 61.6 1.0
O Q:GLY44 4.1 57.3 1.0
C Q:GLY46 4.1 61.6 1.0
CG2 R:THR90 4.2 56.5 1.0
C Q:ALA45 4.2 63.1 1.0
CB R:SER91 4.2 56.8 1.0
CA R:SER91 4.3 56.6 1.0
OP1 S:DG38 4.3 93.3 1.0
CA Q:ALA45 4.6 65.6 1.0
CB Q:ALA47 4.6 64.5 1.0
CA Q:ALA47 4.6 62.6 1.0
N Q:GLY44 4.7 55.8 1.0
OG1 R:THR90 4.7 50.5 1.0
N R:THR90 4.8 53.2 1.0
O R:THR90 5.0 73.0 1.0
O R:ILE89 5.0 60.3 1.0

Reference:

Z.Adhireksan, D.Sharma, B.Qiuye, P.L.Lee, S.Padavattan, C.A.Davey. Linker Histones Associate Heterogeneously with Nucleosomes in the Condensed State To Be Published.
Page generated: Tue Jul 30 13:58:14 2024

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