Chlorine in PDB 5omx: X-Ray Structure of the H2A-N38C Nucleosome Core Particle

The structure of X-Ray Structure of the H2A-N38C Nucleosome Core Particle, PDB code: 5omx was solved by T.D.Frouws, T.J.Richmond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.14 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.753, 182.578, 109.645, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 25.9

The structure of X-Ray Structure of the H2A-N38C Nucleosome Core Particle also contains other interesting chemical elements:

Manganese

(Mn)

33 atoms

The binding sites of Chlorine atom in the X-Ray Structure of the H2A-N38C Nucleosome Core Particle (pdb code 5omx). 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 Structure of the H2A-N38C Nucleosome Core Particle, PDB code: 5omx:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the X-Ray Structure of the H2A-N38C Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:69.3 occ:1.00 N A:LYS122 3.0 40.3 1.0 CD A:PRO121 3.3 49.4 1.0 CG A:LYS122 3.4 52.5 1.0 CB A:LYS122 3.5 45.1 1.0 N A:PRO121 3.5 45.3 1.0 CB A:PRO121 3.6 47.1 1.0 CB A:MET120 3.7 42.4 1.0 CA A:LYS122 3.8 41.3 1.0 C A:PRO121 3.9 39.8 1.0 CD A:LYS122 3.9 58.7 1.0 CA A:PRO121 3.9 45.6 1.0 CG A:PRO121 3.9 48.1 1.0 C A:MET120 4.2 46.6 1.0 CE A:LYS122 4.4 70.3 1.0 CA A:MET120 4.6 50.7 1.0 CG A:MET120 4.7 53.3 1.0 SD A:MET120 4.8 67.0 1.0 O A:MET120 5.0 37.3 1.0

Chlorine binding site 2 out of 4 in the X-Ray Structure of the H2A-N38C Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:57.0 occ:1.00 N C:GLY46 3.2 45.2 1.0 N D:SER91 3.3 46.7 1.0 CA C:GLY46 3.5 34.1 1.0 CB D:THR90 3.6 49.1 1.0 CA D:THR90 3.7 46.9 1.0 N C:ALA47 3.7 36.5 1.0 CA C:GLY44 3.8 49.5 1.0 C C:GLY44 3.8 59.0 1.0 OG D:SER91 4.0 54.9 1.0 N C:ALA45 4.0 53.8 1.0 C D:THR90 4.0 41.3 1.0 C C:GLY46 4.0 40.2 1.0 CG2 D:THR90 4.2 49.1 1.0 CB D:SER91 4.2 34.5 1.0 O C:GLY44 4.2 49.5 1.0 OP1 J:DA38 4.3 79.0 1.0 CA D:SER91 4.4 42.3 1.0 C C:ALA45 4.4 52.1 1.0 OG1 D:THR90 4.7 61.3 1.0 CA C:ALA45 4.7 57.5 1.0 N C:GLY44 4.8 49.1 1.0 CA C:ALA47 4.8 33.4 1.0 CB C:ALA47 5.0 33.0 1.0 O D:ILE89 5.0 62.5 1.0 N D:THR90 5.0 42.0 1.0

Chlorine binding site 3 out of 4 in the X-Ray Structure of the H2A-N38C Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl202 b:69.6 occ:1.00 N E:LYS122 3.1 31.3 1.0 CB E:LYS122 3.4 30.7 1.0 CD E:PRO121 3.6 29.3 1.0 CG E:LYS122 3.6 51.3 1.0 CD E:LYS122 3.6 41.0 1.0 N E:PRO121 3.8 26.4 1.0 CB E:PRO121 3.8 29.9 1.0 CA E:LYS122 3.9 38.4 1.0 CB E:MET120 3.9 35.7 1.0 C E:PRO121 4.1 34.5 1.0 CA E:PRO121 4.1 26.5 1.0 CG E:PRO121 4.2 30.9 1.0 CE E:MET120 4.2 53.7 1.0 C E:MET120 4.4 28.8 1.0 CE E:LYS122 4.7 59.4 1.0 CA E:MET120 4.8 29.4 1.0 CG E:MET120 5.0 45.0 1.0

Chlorine binding site 4 out of 4 in the X-Ray Structure of the H2A-N38C Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure of the H2A-N38C Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:72.1 occ:1.00 N G:GLY46 3.1 60.1 1.0 N G:ALA47 3.5 49.9 1.0 N H:SER91 3.5 52.8 1.0 CA G:GLY46 3.6 50.8 1.0 CA G:GLY44 3.6 59.5 1.0 N G:ALA45 3.6 58.8 1.0 CA H:THR90 3.6 55.0 1.0 C G:GLY44 3.7 62.1 1.0 CB H:THR90 3.7 54.6 1.0 C G:GLY46 4.0 55.8 1.0 C H:THR90 4.0 40.1 1.0 C G:ALA45 4.1 60.1 1.0 OG H:SER91 4.2 67.3 1.0 CG2 H:THR90 4.3 52.1 1.0 O G:GLY44 4.3 67.5 1.0 OP1 I:DA38 4.4 0.5 1.0 CA G:ALA45 4.5 51.6 1.0 CB H:SER91 4.5 55.6 1.0 CA G:ALA47 4.5 50.2 1.0 CB G:ALA47 4.6 52.9 1.0 CA H:SER91 4.6 49.6 1.0 N G:GLY44 4.6 64.1 1.0 O H:ILE89 4.8 58.6 1.0 N H:THR90 4.9 55.6 1.0 OG1 H:THR90 5.0 61.1 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