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Chlorine in PDB 5b0z: The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution

Protein crystallography data

The structure of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution, PDB code: 5b0z was solved by Y.Suzuki, N.Horikoshi, D.Kato, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.94 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.685, 108.204, 168.286, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 25.4

Other elements in 5b0z:

The structure of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution (pdb code 5b0z). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution, PDB code: 5b0z:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5b0z

Go back to Chlorine Binding Sites List in 5b0z
Chlorine binding site 1 out of 4 in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:32.9
occ:0.80
 N A:LYS122 3.2 25.5 1.0
CD A:LYS122 3.4 35.9 1.0
CG A:LYS122 3.4 28.4 1.0
CB A:LYS122 3.5 27.0 1.0
CD A:PRO121 3.6 31.4 1.0
N A:PRO121 3.8 28.6 1.0
CB A:PRO121 3.8 29.8 1.0
CA A:LYS122 3.9 28.1 1.0
CB A:MET120 3.9 23.2 1.0
CG A:PRO121 4.0 24.0 1.0
C A:PRO121 4.0 27.6 1.0
CA A:PRO121 4.1 27.4 1.0
C A:MET120 4.4 29.0 1.0
CE A:LYS122 4.7 33.6 1.0
CA A:MET120 4.7 24.7 1.0
CG A:MET120 4.9 28.3 1.0
SD A:MET120 4.9 33.4 1.0

Chlorine binding site 2 out of 4 in 5b0z

Go back to Chlorine Binding Sites List in 5b0z
Chlorine binding site 2 out of 4 in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:27.7
occ:1.00
 N D:SER91 3.1 23.0 1.0
N C:GLY46 3.2 23.6 1.0
CB D:THR90 3.4 21.3 1.0
CA D:THR90 3.5 26.6 1.0
N C:ALA47 3.5 25.6 1.0
CA C:GLY46 3.6 22.9 1.0
CA C:GLY44 3.7 26.1 1.0
C C:GLY44 3.8 30.9 1.0
C D:THR90 3.8 27.8 1.0
C C:GLY46 3.9 24.6 1.0
N C:ALA45 3.9 28.0 1.0
OG D:SER91 4.0 32.7 1.0
OP1 J:DT258 4.1 40.6 1.0
CB D:SER91 4.1 27.7 1.0
CG2 D:THR90 4.1 23.0 1.0
CA D:SER91 4.2 25.1 1.0
O C:GLY44 4.3 22.1 1.0
C C:ALA45 4.3 23.4 1.0
CA C:ALA47 4.5 25.8 1.0
OG1 D:THR90 4.6 23.5 1.0
N C:GLY44 4.6 22.8 1.0
CB C:ALA47 4.7 19.5 1.0
CA C:ALA45 4.7 26.0 1.0
N D:THR90 4.9 22.5 1.0
O D:ILE89 4.9 23.3 1.0
O C:GLY46 4.9 21.5 1.0

Chlorine binding site 3 out of 4 in 5b0z

Go back to Chlorine Binding Sites List in 5b0z
Chlorine binding site 3 out of 4 in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:25.6
occ:0.88
 N E:LYS122 3.2 22.7 1.0
CD E:PRO121 3.5 24.4 1.0
CG E:LYS122 3.6 24.9 1.0
N E:PRO121 3.6 23.9 1.0
CB E:LYS122 3.8 20.8 1.0
CB E:MET120 3.8 18.5 1.0
CB E:PRO121 3.8 23.8 1.0
C E:PRO121 4.0 25.1 1.0
CG E:PRO121 4.0 25.8 1.0
CA E:LYS122 4.0 24.6 1.0
CA E:PRO121 4.0 20.9 1.0
C E:MET120 4.3 20.9 1.0
CE E:LYS122 4.3 31.7 1.0
CD E:LYS122 4.5 28.7 1.0
CA E:MET120 4.6 20.1 1.0
CG E:MET120 4.8 22.2 1.0
SD E:MET120 4.8 30.2 1.0

Chlorine binding site 4 out of 4 in 5b0z

Go back to Chlorine Binding Sites List in 5b0z
Chlorine binding site 4 out of 4 in the The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of the Nucleosome Containing H3.2, at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl301

b:28.9
occ:1.00
 O I:HOH436 2.9 41.7 1.0
N G:GLY46 3.1 20.8 1.0
N H:SER91 3.2 22.0 1.0
N G:ALA47 3.4 20.2 1.0
CA G:GLY46 3.5 24.3 1.0
CA H:THR90 3.5 25.8 1.0
CB H:THR90 3.5 23.8 1.0
CA G:GLY44 3.6 27.2 1.0
C G:GLY44 3.6 27.2 1.0
N G:ALA45 3.7 24.7 1.0
C H:THR90 3.8 24.4 1.0
C G:GLY46 3.8 23.0 1.0
OG H:SER91 4.0 29.3 1.0
OP1 I:DA111 4.0 43.6 1.0
CB H:SER91 4.1 24.4 1.0
CG2 H:THR90 4.2 24.1 1.0
C G:ALA45 4.2 24.5 1.0
O G:GLY44 4.2 26.7 1.0
CA H:SER91 4.2 24.3 1.0
CA G:ALA47 4.5 21.5 1.0
CA G:ALA45 4.6 29.1 1.0
N G:GLY44 4.6 27.4 1.0
CB G:ALA47 4.6 19.7 1.0
OG1 H:THR90 4.7 24.1 1.0
N H:THR90 4.9 22.1 1.0
O G:GLY46 4.9 23.4 1.0
O I:HOH440 5.0 45.2 1.0
O H:THR90 5.0 24.5 1.0
O H:ILE89 5.0 24.6 1.0

Reference:

Y.Suzuki, N.Horikoshi, D.Kato, H.Kurumizaka. Crystal Structure of the Nucleosome Containing Histone H3 with Crotonylated Lysine 122 Biochem.Biophys.Res.Commun. V. 469 483 2016.
ISSN: ESSN 1090-2104
PubMed: 26694698
DOI: 10.1016/J.BBRC.2015.12.041
Page generated: Sat Jul 12 00:21:27 2025

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