Chlorine in PDB 6v2k: The Nucleosome Structure After H2A-H2B Exchange

The structure of The Nucleosome Structure After H2A-H2B Exchange, PDB code: 6v2k was solved by Y.Arimura, R.Hirano, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.72 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.561, 107.711, 168.158, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.9

The structure of The Nucleosome Structure After H2A-H2B Exchange also contains other interesting chemical elements:

Manganese

(Mn)

10 atoms

The binding sites of Chlorine atom in the The Nucleosome Structure After H2A-H2B Exchange (pdb code 6v2k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the The Nucleosome Structure After H2A-H2B Exchange, PDB code: 6v2k:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the The Nucleosome Structure After H2A-H2B Exchange


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2001 b:69.4 occ:1.00 N A:LYS122 3.3 42.8 1.0 CG A:LYS122 3.4 47.5 1.0 CD A:PRO121 3.6 53.6 1.0 CB A:LYS122 3.7 37.5 1.0 N A:PRO121 3.8 53.1 1.0 CB A:MET120 3.9 37.8 1.0 CB A:PRO121 3.9 46.3 1.0 CD A:LYS122 4.1 47.4 1.0 CG A:PRO121 4.1 48.5 1.0 CA A:LYS122 4.1 43.8 1.0 C A:PRO121 4.2 48.9 1.0 CA A:PRO121 4.2 54.6 1.0 CE A:LYS122 4.3 51.2 1.0 C A:MET120 4.4 50.3 1.0 CA A:MET120 4.7 39.0 1.0 CG A:MET120 4.9 60.1 1.0 SD A:MET120 4.9 60.4 1.0

Chlorine binding site 2 out of 4 in the The Nucleosome Structure After H2A-H2B Exchange


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:47.1 occ:1.00 N C:GLY46 2.9 38.5 1.0 N D:SER91 3.3 33.8 1.0 CA C:GLY46 3.3 37.1 1.0 N C:ALA47 3.6 41.4 1.0 CB D:THR90 3.6 39.5 1.0 CA D:THR90 3.6 45.0 1.0 C C:GLY44 3.6 41.5 1.0 N C:ALA45 3.7 42.9 1.0 CA C:GLY44 3.7 41.5 1.0 C C:GLY46 3.8 39.5 1.0 C D:THR90 4.0 47.2 1.0 OP1 J:DT258 4.0 57.0 1.0 C C:ALA45 4.1 44.7 1.0 CB D:SER91 4.2 41.4 1.0 O C:GLY44 4.2 48.4 1.0 OG D:SER91 4.2 53.6 1.0 CG2 D:THR90 4.3 29.2 1.0 CA D:SER91 4.3 43.6 1.0 CA C:ALA45 4.5 48.5 1.0 CA C:ALA47 4.7 39.2 1.0 OG1 D:THR90 4.7 42.3 1.0 N C:GLY44 4.8 40.2 1.0 CB C:ALA47 4.9 29.7 1.0 O D:ILE89 4.9 45.3 1.0 N D:THR90 4.9 36.9 1.0 O C:GLY46 4.9 44.0 1.0

Chlorine binding site 3 out of 4 in the The Nucleosome Structure After H2A-H2B Exchange


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl202 b:62.2 occ:1.00 N E:LYS122 3.1 35.6 1.0 CD E:PRO121 3.4 47.1 1.0 CB E:PRO121 3.4 40.7 1.0 N E:PRO121 3.6 50.4 1.0 CG E:PRO121 3.8 42.7 1.0 CG E:LYS122 3.8 40.7 1.0 CA E:PRO121 3.8 40.8 1.0 CB E:LYS122 3.9 28.6 1.0 C E:PRO121 3.9 47.4 1.0 CA E:LYS122 4.0 41.0 1.0 CB E:MET120 4.0 38.3 1.0 C E:MET120 4.3 44.4 1.0 CD E:LYS122 4.7 38.4 1.0 CA E:MET120 4.7 39.1 1.0

Chlorine binding site 4 out of 4 in the The Nucleosome Structure After H2A-H2B Exchange


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:58.0 occ:1.00 N G:GLY46 3.1 41.8 1.0 N H:SER91 3.3 31.0 1.0 CA G:GLY46 3.5 42.4 1.0 N G:ALA47 3.6 35.4 1.0 CB H:THR90 3.6 36.4 1.0 CA G:GLY44 3.7 37.4 1.0 CA H:THR90 3.7 44.6 1.0 N G:ALA45 3.7 42.4 1.0 C G:GLY44 3.7 38.5 1.0 OP1 I:DA111 3.8 48.9 1.0 C G:GLY46 4.0 44.1 1.0 C H:THR90 4.0 41.2 1.0 OG H:SER91 4.2 48.6 1.0 C G:ALA45 4.2 43.4 1.0 CB H:SER91 4.2 38.7 1.0 CG2 H:THR90 4.2 31.3 1.0 CA H:SER91 4.4 40.7 1.0 O G:GLY44 4.4 47.4 1.0 CA G:ALA45 4.5 41.9 1.0 CA G:ALA47 4.6 42.7 1.0 N G:GLY44 4.7 45.3 1.0 CB G:ALA47 4.7 38.1 1.0 OG1 H:THR90 4.8 44.8 1.0 O H:ILE89 5.0 39.5 1.0 N H:THR90 5.0 42.2 1.0

R.Hirano, A.Yasuhiro, H.Kurumizaka. A Histone Variant H2A.B Complexed with H2B Is Spontaneously Exchanged By Canonical H2A-H2B in the Nucleosome To Be Published.