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

Go back to Chlorine Binding Sites List in 8yti
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

Go back to Chlorine Binding Sites List in 8yti
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

Go back to Chlorine Binding Sites List in 8yti
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

Go back to Chlorine Binding Sites List in 8yti
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

Go back to Chlorine Binding Sites List in 8yti
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

Go back to Chlorine Binding Sites List in 8yti
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

Go back to Chlorine Binding Sites List in 8yti
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

Go back to Chlorine Binding Sites List in 8yti
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

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy