Chlorine in PDB 5y0c: Crystal Structure of the Human Nucleosome at 2.09 Angstrom Resolution

The structure of Crystal Structure of the Human Nucleosome at 2.09 Angstrom Resolution, PDB code: 5y0c was solved by H.Kurumizaka, Y.Arimura, R.Fujita, M.Noda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.913, 107.103, 167.003, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.9

The structure of Crystal Structure of the Human Nucleosome at 2.09 Angstrom Resolution also contains other interesting chemical elements:

Manganese

(Mn)

10 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Human Nucleosome at 2.09 Angstrom Resolution (pdb code 5y0c). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Human Nucleosome at 2.09 Angstrom Resolution, PDB code: 5y0c:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Human Nucleosome at 2.09 Angstrom Resolution


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 the Human Nucleosome at 2.09 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2001 b:39.1 occ:1.00 N A:LYS122 3.3 28.6 1.0 CD A:PRO121 3.5 29.0 1.0 CG A:LYS122 3.6 29.9 1.0 CB A:LYS122 3.7 27.3 1.0 N A:PRO121 3.7 29.1 1.0 CB A:MET120 3.8 28.6 1.0 CB A:PRO121 3.9 29.2 1.0 CG A:PRO121 4.0 27.1 1.0 CA A:LYS122 4.1 29.8 1.0 CA A:PRO121 4.2 28.8 1.0 C A:PRO121 4.2 29.3 1.0 CD A:LYS122 4.2 33.0 1.0 C A:MET120 4.4 29.4 1.0 CE A:LYS122 4.5 38.2 1.0 CA A:MET120 4.6 24.3 1.0 CG A:MET120 4.7 30.3 1.0 SD A:MET120 4.8 36.7 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Human Nucleosome at 2.09 Angstrom Resolution


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 the Human Nucleosome at 2.09 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:32.5 occ:1.00 N C:GLY46 3.1 30.0 1.0 N D:SER91 3.2 26.3 1.0 CA C:GLY46 3.5 28.8 1.0 N C:ALA47 3.6 27.7 1.0 CB D:THR90 3.6 32.1 1.0 CA D:THR90 3.7 28.8 1.0 CA C:GLY44 3.7 32.2 1.0 C C:GLY44 3.8 33.1 1.0 N C:ALA45 3.8 33.5 1.0 C C:GLY46 3.9 27.1 1.0 C D:THR90 4.0 30.4 1.0 OP1 J:DT258 4.0 48.3 1.0 CB D:SER91 4.0 27.7 1.0 OG D:SER91 4.1 35.5 1.0 CA D:SER91 4.2 26.9 1.0 C C:ALA45 4.3 30.0 1.0 O C:GLY44 4.3 30.9 1.0 CG2 D:THR90 4.4 29.2 1.0 CA C:ALA47 4.6 25.3 1.0 CA C:ALA45 4.6 30.8 1.0 CB C:ALA47 4.7 22.0 1.0 N C:GLY44 4.7 32.4 1.0 OG1 D:THR90 4.7 27.1 1.0 O C:GLY46 4.9 26.7 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Human Nucleosome at 2.09 Angstrom Resolution


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 the Human Nucleosome at 2.09 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl202 b:37.6 occ:1.00 N E:LYS122 3.4 26.0 1.0 CD E:PRO121 3.4 22.9 1.0 CG E:LYS122 3.7 30.4 1.0 N E:PRO121 3.7 21.2 1.0 CB E:PRO121 3.8 26.0 1.0 CB E:LYS122 3.8 22.1 1.0 CB E:MET120 3.9 25.8 1.0 CG E:PRO121 3.9 27.8 1.0 CA E:PRO121 4.1 26.1 1.0 CA E:LYS122 4.2 26.9 1.0 C E:PRO121 4.2 25.2 1.0 CD E:LYS122 4.3 33.2 1.0 C E:MET120 4.4 21.8 1.0 CE E:LYS122 4.6 39.5 1.0 CA E:MET120 4.7 22.9 1.0 CG E:MET120 4.8 26.8 1.0 SD E:MET120 4.9 32.3 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Human Nucleosome at 2.09 Angstrom Resolution


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 the Human Nucleosome at 2.09 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:27.1 occ:1.00 O I:HOH303 3.0 38.8 1.0 N H:SER91 3.2 20.3 1.0 O H:HOH215 3.3 36.7 1.0 N G:GLY46 3.3 31.1 1.0 N G:ALA47 3.5 24.4 1.0 CB H:THR90 3.6 23.0 1.0 CA H:THR90 3.6 23.3 1.0 CA G:GLY46 3.6 28.1 1.0 CA G:GLY44 3.7 31.7 1.0 C G:GLY44 3.8 31.4 1.0 C H:THR90 3.9 25.2 1.0 N G:ALA45 3.9 31.6 1.0 C G:GLY46 3.9 26.0 1.0 CB H:SER91 4.0 25.9 1.0 OP1 I:DA111 4.0 50.4 1.0 OG H:SER91 4.1 35.5 1.0 CA H:SER91 4.2 25.8 1.0 CG2 H:THR90 4.3 25.0 1.0 O G:GLY44 4.3 31.3 1.0 C G:ALA45 4.4 31.4 1.0 CA G:ALA47 4.5 24.9 1.0 CB G:ALA47 4.5 20.7 1.0 N G:GLY44 4.7 29.3 1.0 OG1 H:THR90 4.7 28.8 1.0 CA G:ALA45 4.7 32.1 1.0 O H:ILE89 4.9 28.5 1.0 N H:THR90 4.9 23.2 1.0 O G:GLY46 5.0 26.4 1.0

Y.Arimura, M.Ikura, R.Fujita, M.Noda, W.Kobayashi, N.Horikoshi, J.Sun, L.Shi, M.Kusakabe, M.Harata, Y.Ohkawa, S.Tashiro, H.Kimura, T.Ikura, H.Kurumizaka. Cancer-Associated Mutations of Histones H2B, H3.1 and H2A.Z.1 Affect the Structure and Stability of the Nucleosome. Nucleic Acids Res. V. 46 10007 2018.
ISSN: ESSN 1362-4962
PubMed: 30053102
DOI: 10.1093/NAR/GKY661