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

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

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

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 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 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 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 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

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