Chlorine in PDB 6k1j: Human Nucleosome Core Particle with H2A.X Variant

The structure of Human Nucleosome Core Particle with H2A.X Variant, PDB code: 6k1j was solved by D.Sharma, L.De Falco, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.88 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.750, 109.940, 180.370, 90.00, 90.00, 90.00
R / Rfree (%)	26.5 / 31.9

The structure of Human Nucleosome Core Particle with H2A.X Variant also contains other interesting chemical elements:

Manganese

(Mn)

12 atoms

The binding sites of Chlorine atom in the Human Nucleosome Core Particle with H2A.X Variant (pdb code 6k1j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human Nucleosome Core Particle with H2A.X Variant, PDB code: 6k1j:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Human Nucleosome Core Particle with H2A.X Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Nucleosome Core Particle with H2A.X Variant within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:59.6 occ:1.00 N C:GLY46 3.1 55.6 1.0 C C:GLY44 3.4 62.5 1.0 CA C:GLY46 3.4 57.8 1.0 CA C:GLY44 3.4 64.9 1.0 N D:SER88 3.5 54.5 1.0 N C:ALA45 3.5 69.3 1.0 N C:ALA47 3.6 60.8 1.0 CB D:THR87 3.7 62.8 1.0 CA D:THR87 3.7 58.6 1.0 O C:GLY44 3.9 65.3 1.0 C C:GLY46 3.9 62.7 1.0 OG D:SER88 4.0 50.5 1.0 OP1 J:DA37 4.0 99.3 1.0 C D:THR87 4.1 59.7 1.0 C C:ALA45 4.2 65.7 1.0 CB D:SER88 4.3 51.1 1.0 CG2 D:THR87 4.4 67.2 1.0 CA C:ALA45 4.5 73.0 1.0 CA D:SER88 4.5 53.8 1.0 N C:GLY44 4.6 64.9 1.0 CA C:ALA47 4.7 60.3 1.0 OG1 D:THR87 4.8 62.1 1.0 CB C:ALA47 4.9 63.5 1.0

Chlorine binding site 2 out of 2 in the Human Nucleosome Core Particle with H2A.X Variant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Nucleosome Core Particle with H2A.X Variant within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl201 b:71.2 occ:1.00 N G:GLY46 3.3 71.5 1.0 N H:SER88 3.4 63.3 1.0 OG H:SER88 3.5 73.6 1.0 CA G:GLY46 3.6 73.1 1.0 CB H:THR87 3.6 58.3 1.0 CA G:GLY44 3.7 67.7 1.0 CA H:THR87 3.7 62.6 1.0 OP1 I:DT38 3.7 96.1 1.0 C G:GLY44 3.7 68.4 1.0 N G:ALA47 3.7 75.9 1.0 N G:ALA45 4.0 75.8 1.0 C H:THR87 4.0 63.1 1.0 O G:GLY44 4.1 60.0 1.0 C G:GLY46 4.1 77.7 1.0 CB H:SER88 4.3 70.7 1.0 CG2 H:THR87 4.3 57.0 1.0 C G:ALA45 4.4 77.6 1.0 CA H:SER88 4.5 66.8 1.0 N G:GLY44 4.7 69.5 1.0 OG1 H:THR87 4.7 49.5 1.0 CA G:ALA47 4.8 67.0 1.0 CA G:ALA45 4.8 79.1 1.0 CB G:ALA47 4.8 63.5 1.0

D.Sharma, L.De Falco, S.Padavattan, C.Rao, S.Geifman-Shochat, C.F.Liu, C.A.Davey. PARP1 Exhibits Enhanced Association and Catalytic Efficiency with Gamma H2A.X-Nucleosome. Nat Commun V. 10 5751 2019.
ISSN: ESSN 2041-1723
PubMed: 31848352
DOI: 10.1038/S41467-019-13641-0