Chlorine in PDB 6kvd: Crystal Structure of Human Nucleosome Containing H2A.J

The structure of Crystal Structure of Human Nucleosome Containing H2A.J, PDB code: 6kvd was solved by H.Tanaka, M.Koyama, S.Sato, T.Kujirai, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.84 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.640, 108.791, 171.177, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.7

The structure of Crystal Structure of Human Nucleosome Containing H2A.J also contains other interesting chemical elements:

Manganese

(Mn)

13 atoms

The binding sites of Chlorine atom in the Crystal Structure of Human Nucleosome Containing H2A.J (pdb code 6kvd). 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 Human Nucleosome Containing H2A.J, PDB code: 6kvd:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:51.9 occ:1.00 N A:LYS122 3.2 38.3 1.0 CD A:PRO121 3.4 42.4 1.0 N A:PRO121 3.6 42.9 1.0 CG A:LYS122 3.7 36.7 1.0 CB A:LYS122 3.8 40.2 1.0 CB A:PRO121 3.8 42.6 1.0 CB A:MET120 3.8 35.3 1.0 CG A:PRO121 3.9 41.5 1.0 CE A:LYS122 4.0 45.3 1.0 C A:PRO121 4.1 38.1 1.0 CA A:PRO121 4.1 37.3 1.0 CA A:LYS122 4.1 37.0 1.0 C A:MET120 4.2 37.8 1.0 CD A:LYS122 4.3 44.3 1.0 CA A:MET120 4.6 36.8 1.0 CG A:MET120 4.8 38.3 1.0 SD A:MET120 4.9 47.3 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl202 b:37.8 occ:1.00 N D:SER91 3.2 30.6 1.0 N C:GLY46 3.2 34.6 1.0 CB D:THR90 3.5 33.7 1.0 CA D:THR90 3.5 31.5 1.0 N C:ALA47 3.6 30.4 1.0 CA C:GLY46 3.6 25.7 1.0 N C:ALA45 3.8 32.0 1.0 C C:GLY44 3.8 37.2 1.0 CA C:GLY44 3.8 34.7 1.0 C D:THR90 3.9 33.4 1.0 C C:GLY46 4.0 31.8 1.0 OP1 J:DT258 4.1 53.0 1.0 CB D:SER91 4.1 29.7 1.0 CG2 D:THR90 4.1 29.1 1.0 OG D:SER91 4.2 35.3 1.0 CA D:SER91 4.2 31.7 1.0 C C:ALA45 4.3 29.1 1.0 O C:GLY44 4.4 32.3 1.0 CA C:ALA47 4.6 32.2 1.0 OG1 D:THR90 4.6 32.8 1.0 CA C:ALA45 4.6 31.1 1.0 CB C:ALA47 4.7 23.1 1.0 N C:GLY44 4.8 36.2 1.0 N D:THR90 4.9 30.6 1.0 O D:ILE89 5.0 33.5 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl201 b:52.1 occ:1.00 CG E:LYS122 3.4 35.9 1.0 N E:LYS122 3.4 33.2 1.0 CD E:PRO121 3.8 30.1 1.0 CB E:LYS122 3.8 31.5 1.0 N E:PRO121 3.8 33.5 1.0 CB E:MET120 3.9 33.3 1.0 CB E:PRO121 3.9 33.9 1.0 CE E:LYS122 4.0 47.3 1.0 CG E:PRO121 4.2 34.9 1.0 CD E:LYS122 4.2 46.1 1.0 CA E:LYS122 4.2 38.2 1.0 CA E:PRO121 4.3 29.8 1.0 C E:PRO121 4.3 37.7 1.0 C E:MET120 4.4 35.1 1.0 CA E:MET120 4.7 28.8 1.0 CG E:MET120 4.8 30.3 1.0 SD E:MET120 4.9 46.1 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:34.4 occ:1.00 N G:GLY46 3.1 28.5 1.0 N H:SER91 3.2 25.7 1.0 N G:ALA47 3.5 30.2 1.0 CA H:THR90 3.5 26.2 1.0 CA G:GLY46 3.6 30.8 1.0 CB H:THR90 3.6 32.6 1.0 C G:GLY44 3.7 38.6 1.0 CA G:GLY44 3.7 36.9 1.0 N G:ALA45 3.8 37.0 1.0 C H:THR90 3.9 28.4 1.0 C G:GLY46 3.9 30.2 1.0 CB H:SER91 4.1 33.9 1.0 O G:GLY44 4.2 34.9 1.0 OP1 I:DA111 4.2 50.8 1.0 C G:ALA45 4.2 32.0 1.0 CG2 H:THR90 4.2 24.4 1.0 CA H:SER91 4.3 32.9 1.0 OG H:SER91 4.3 39.4 1.0 CA G:ALA47 4.5 28.9 1.0 CB G:ALA47 4.5 31.1 1.0 N G:GLY44 4.6 31.9 1.0 CA G:ALA45 4.6 37.3 1.0 O H:ILE89 4.8 28.5 1.0 OG1 H:THR90 4.8 31.7 1.0 N H:THR90 4.9 27.5 1.0 O G:GLY46 5.0 29.6 1.0

H.Tanaka, S.Sato, M.Koyama, T.Kujirai, H.Kurumizaka. Biochemical and Structural Analyses of the Nucleosome Containing Human Histone H2A.J. J.Biochem. 2019.
ISSN: ISSN 0021-924X
PubMed: 31793981
DOI: 10.1093/JB/MVZ109