Chlorine in PDB 5ong: X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer

The structure of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer, PDB code: 5ong was solved by T.D.Frouws, P.D.Barth, T.J.Richmond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.50 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.240, 183.130, 109.490, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.7

The structure of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer also contains other interesting chemical elements:

Manganese

(Mn)

20 atoms

The binding sites of Chlorine atom in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer (pdb code 5ong). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer, PDB code: 5ong:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:50.1 occ:0.54 N A:LYS122 3.3 56.5 1.0 CD A:PRO121 3.3 56.5 1.0 N A:PRO121 3.4 48.4 1.0 CB A:PRO121 3.6 59.4 1.0 CG A:PRO121 3.7 63.5 1.0 CB A:MET120 3.7 57.5 1.0 CA A:PRO121 3.9 52.2 1.0 CB A:LYS122 3.9 66.8 1.0 CG A:LYS122 3.9 76.9 1.0 C A:PRO121 4.0 57.3 1.0 C A:MET120 4.1 53.2 1.0 CA A:LYS122 4.2 57.0 1.0 CD A:LYS122 4.3 92.4 1.0 CA A:MET120 4.4 58.1 1.0 CE A:MET120 4.8 63.5 1.0 O A:MET120 4.8 56.5 1.0 CG A:MET120 4.9 62.0 1.0 SD A:MET120 4.9 71.6 1.0

Chlorine binding site 2 out of 4 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl201 b:68.6 occ:1.00 N D:SER88 3.2 49.3 1.0 N C:GLY46 3.4 46.4 1.0 CB D:THR87 3.4 54.8 1.0 CA D:THR87 3.5 53.1 1.0 CA C:GLY46 3.7 52.4 1.0 OG D:SER88 3.8 53.3 1.0 C D:THR87 3.8 49.4 1.0 N C:ALA47 3.9 49.9 1.0 CA C:GLY44 4.0 59.4 1.0 C C:GLY44 4.1 62.1 1.0 OP1 J:DA38 4.1 71.0 1.0 CB D:SER88 4.1 51.6 1.0 N C:ALA45 4.2 60.2 1.0 CG2 D:THR87 4.2 46.3 1.0 C C:GLY46 4.2 56.7 1.0 CA D:SER88 4.2 49.1 1.0 OG1 D:THR87 4.6 66.3 1.0 C C:ALA45 4.6 54.3 1.0 O C:GLY44 4.7 60.4 1.0 N D:THR87 4.9 51.6 1.0 CA C:ALA47 4.9 42.5 1.0 N C:GLY44 4.9 54.4 1.0 CA C:ALA45 5.0 57.4 1.0

Chlorine binding site 3 out of 4 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl202 b:53.1 occ:0.72 NZ E:LYS122 3.2 70.0 1.0 N E:LYS122 3.3 44.6 1.0 CD E:PRO121 3.4 41.9 1.0 N E:PRO121 3.6 48.6 1.0 CB E:PRO121 3.7 31.1 1.0 CG E:LYS122 3.8 68.3 1.0 CG E:PRO121 3.8 36.1 1.0 CE E:LYS122 3.9 70.9 1.0 CB E:LYS122 3.9 56.9 1.0 CB E:MET120 3.9 33.8 1.0 CE E:MET120 4.0 62.6 1.0 CA E:PRO121 4.1 43.1 1.0 C E:PRO121 4.1 48.9 1.0 CA E:LYS122 4.2 46.6 1.0 C E:MET120 4.3 40.2 1.0 CD E:LYS122 4.4 70.5 1.0 CA E:MET120 4.7 36.9 1.0 CG E:MET120 4.9 40.5 1.0 SD E:MET120 5.0 54.4 1.0

Chlorine binding site 4 out of 4 in the X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:63.5 occ:1.00 N G:GLY46 3.3 70.6 1.0 N H:SER88 3.5 48.8 1.0 CA G:GLY44 3.6 66.0 1.0 CA H:THR87 3.6 54.5 1.0 CB H:THR87 3.7 53.1 1.0 C G:GLY44 3.7 68.3 1.0 CA G:GLY46 3.8 72.0 1.0 N G:ALA47 3.8 67.7 1.0 N G:ALA45 3.8 70.2 1.0 CG2 H:THR87 4.0 48.2 1.0 OG H:SER88 4.0 80.5 1.0 C H:THR87 4.1 61.4 1.0 C G:GLY46 4.2 74.8 1.0 OP1 I:DA38 4.3 0.3 1.0 O G:GLY44 4.4 70.5 1.0 CB H:SER88 4.4 74.5 1.0 C G:ALA45 4.5 74.1 1.0 CA H:SER88 4.5 58.9 1.0 N G:GLY44 4.6 66.4 1.0 CA G:ALA45 4.7 71.2 1.0 O H:ILE86 4.8 68.0 1.0 CA G:ALA47 4.9 62.7 1.0 CB G:ALA47 4.9 61.6 1.0 N H:THR87 4.9 58.8 1.0

T.D.Frouws, P.D.Barth, T.J.Richmond. Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability. J. Mol. Biol. V. 430 45 2018.
ISSN: ESSN 1089-8638
PubMed: 29113904
DOI: 10.1016/J.JMB.2017.10.029