Chlorine in PDB 5onw: X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer and the Two H2A/H2B Dimers Crosslinked Via H2A N38C

The structure of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer and the Two H2A/H2B Dimers Crosslinked Via H2A N38C, PDB code: 5onw 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)	29.51 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.560, 183.830, 109.490, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.4

The structure of X-Ray Crystal Structure of A Nucleosome Core Particle with Its Dna Site-Specifically Crosslinked to the Histone Octamer and the Two H2A/H2B Dimers Crosslinked Via H2A N38C 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 and the Two H2A/H2B Dimers Crosslinked Via H2A N38C (pdb code 5onw). 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 and the Two H2A/H2B Dimers Crosslinked Via H2A N38C, PDB code: 5onw:
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 and the Two H2A/H2B Dimers Crosslinked Via H2A N38C


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 and the Two H2A/H2B Dimers Crosslinked Via H2A N38C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:82.3 occ:1.00 N A:LYS122 3.2 54.9 1.0 CG A:PRO121 3.3 53.7 1.0 CG A:LYS122 3.4 80.7 1.0 CB A:LYS122 3.6 55.5 1.0 CE A:MET120 3.7 88.6 1.0 CD A:PRO121 3.7 71.5 1.0 N A:PRO121 3.8 58.7 1.0 CB A:MET120 3.9 54.9 1.0 CA A:LYS122 4.0 56.0 1.0 CB A:PRO121 4.0 53.8 1.0 C A:PRO121 4.0 60.8 1.0 CA A:PRO121 4.2 69.3 1.0 NZ A:LYS122 4.2 78.8 1.0 C A:MET120 4.3 63.6 1.0 CD A:LYS122 4.6 95.8 1.0 CE A:LYS122 4.6 76.3 1.0 CA A:MET120 4.6 60.8 1.0 CG A:MET120 4.7 79.4 1.0 O A:MET120 5.0 73.2 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 and the Two H2A/H2B Dimers Crosslinked Via H2A N38C


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 and the Two H2A/H2B Dimers Crosslinked Via H2A N38C within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:73.0 occ:1.00 O D:HOH302 2.3 63.6 1.0 N C:GLY46 3.2 62.3 1.0 N D:SER88 3.3 47.3 1.0 CA D:THR87 3.6 59.5 1.0 CA C:GLY44 3.6 70.4 1.0 C C:GLY44 3.6 67.2 1.0 CA C:GLY46 3.6 60.3 1.0 N C:ALA47 3.7 78.3 1.0 N C:ALA45 3.8 59.5 1.0 C D:THR87 3.9 70.3 1.0 CB D:THR87 4.0 66.7 1.0 OP1 J:DA38 4.0 66.7 1.0 C C:GLY46 4.1 77.2 1.0 O C:GLY44 4.1 61.6 1.0 OG D:SER88 4.2 61.7 1.0 CB D:SER88 4.3 63.0 1.0 CG2 D:THR87 4.3 81.7 1.0 C C:ALA45 4.4 73.7 1.0 CA D:SER88 4.4 55.0 1.0 N C:GLY44 4.5 88.6 1.0 O D:ILE86 4.6 51.1 1.0 CA C:ALA45 4.7 66.5 1.0 CA C:ALA47 4.7 67.2 1.0 CB C:ALA47 4.7 61.9 1.0 N D:THR87 4.8 74.2 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 and the Two H2A/H2B Dimers Crosslinked Via H2A N38C


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 and the Two H2A/H2B Dimers Crosslinked Via H2A N38C within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl202 b:85.3 occ:1.00 N E:LYS122 3.1 41.0 1.0 CG E:LYS122 3.4 80.3 1.0 CB E:LYS122 3.5 47.9 1.0 CD E:PRO121 3.6 50.5 1.0 N E:PRO121 3.6 56.2 1.0 CE E:LYS122 3.7 0.2 1.0 CB E:MET120 3.8 51.7 1.0 CB E:PRO121 3.8 41.4 1.0 CA E:LYS122 3.8 49.7 1.0 C E:PRO121 4.0 45.7 1.0 CA E:PRO121 4.0 38.4 1.0 CG E:PRO121 4.0 46.6 1.0 CE E:MET120 4.1 68.2 1.0 CD E:LYS122 4.1 83.9 1.0 C E:MET120 4.2 52.4 1.0 CA E:MET120 4.6 60.5 1.0 O E:HOH309 4.6 83.0 1.0 NZ E:LYS122 4.8 0.6 1.0 CG E:MET120 4.9 47.7 1.0 O E:MET120 5.0 60.3 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 and the Two H2A/H2B Dimers Crosslinked Via H2A N38C


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 and the Two H2A/H2B Dimers Crosslinked Via H2A N38C within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:70.2 occ:1.00 N G:GLY46 3.3 70.2 1.0 N H:SER88 3.4 68.5 1.0 CA G:GLY44 3.4 59.4 1.0 CA H:THR87 3.5 63.5 1.0 C G:GLY44 3.6 79.5 1.0 N G:ALA47 3.7 71.8 1.0 CA G:GLY46 3.7 62.2 1.0 CB H:THR87 3.8 82.1 1.0 N G:ALA45 3.9 85.6 1.0 C H:THR87 3.9 69.6 1.0 O G:GLY44 4.0 69.9 1.0 OP1 I:DA38 4.0 0.2 1.0 CG2 H:THR87 4.1 62.9 1.0 C G:GLY46 4.1 78.3 1.0 OG H:SER88 4.2 73.3 1.0 N G:GLY44 4.2 73.4 1.0 C G:ALA45 4.4 91.9 1.0 CB H:SER88 4.5 77.5 1.0 CA H:SER88 4.5 76.1 1.0 O H:ILE86 4.6 86.2 1.0 CB G:ALA47 4.6 58.4 1.0 CA G:ALA47 4.7 56.1 1.0 N H:THR87 4.7 79.9 1.0 CA G:ALA45 4.8 82.2 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