Chlorine in PDB 5b32: The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3.

The structure of The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3., PDB code: 5b32 was solved by N.Horikoshi, H.Taguchi, Y.Arimura, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.09 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.182, 105.823, 166.263, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 25.9

The structure of The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3. also contains other interesting chemical elements:

Manganese

(Mn)

10 atoms

The binding sites of Chlorine atom in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3. (pdb code 5b32). 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 Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3., PDB code: 5b32:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:54.7 occ:1.00 N A:LYS122 3.2 31.7 1.0 CD A:PRO121 3.4 32.6 1.0 CE A:LYS122 3.5 44.0 1.0 CB A:PRO121 3.6 39.4 1.0 N A:PRO121 3.6 36.4 1.0 CB A:LYS122 3.7 29.3 1.0 CG A:LYS122 3.7 41.1 1.0 CG A:PRO121 3.8 29.9 1.0 CB A:MET120 3.8 31.5 1.0 CA A:PRO121 4.0 33.2 1.0 CA A:LYS122 4.0 32.8 1.0 C A:PRO121 4.1 35.7 1.0 CD A:LYS122 4.2 43.0 1.0 C A:MET120 4.3 32.6 1.0 CA A:MET120 4.6 30.2 1.0 CG A:MET120 4.7 33.4 1.0 SD A:MET120 4.7 48.6 1.0 NZ A:LYS122 4.7 57.8 1.0

Chlorine binding site 2 out of 4 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3. within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:42.6 occ:1.00 N C:GLY46 3.2 35.4 1.0 N D:SER91 3.3 33.7 1.0 CB D:THR90 3.5 32.6 1.0 CA C:GLY44 3.5 37.8 1.0 N C:ALA47 3.6 38.4 1.0 N C:ALA45 3.6 40.8 1.0 CA C:GLY46 3.6 36.4 1.0 CA D:THR90 3.6 33.9 1.0 C C:GLY44 3.7 44.3 1.0 OG D:SER91 3.8 42.7 1.0 OP1 J:DT258 3.8 50.1 1.0 C D:THR90 3.9 31.8 1.0 C C:GLY46 4.0 38.0 1.0 CG2 D:THR90 4.0 29.4 1.0 CB D:SER91 4.1 37.6 1.0 C C:ALA45 4.2 36.4 1.0 CA D:SER91 4.3 36.0 1.0 O C:GLY44 4.4 37.7 1.0 CA C:ALA45 4.5 36.5 1.0 CA C:ALA47 4.5 34.0 1.0 CB C:ALA47 4.6 33.9 1.0 N C:GLY44 4.6 36.3 1.0 OG1 D:THR90 4.7 33.8 1.0 O C:GLY46 5.0 33.8 1.0

Chlorine binding site 3 out of 4 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3. within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl302 b:43.4 occ:1.00 N E:LYS122 3.4 30.1 1.0 CB E:LYS122 3.5 33.4 1.0 CD E:PRO121 3.6 23.3 1.0 CB E:MET120 3.7 28.0 1.0 N E:PRO121 3.9 24.1 1.0 CE E:LYS122 4.0 39.3 1.0 CB E:PRO121 4.0 32.2 1.0 CA E:LYS122 4.0 31.2 1.0 CG E:PRO121 4.1 34.5 1.0 C E:PRO121 4.4 27.6 1.0 CA E:PRO121 4.4 31.1 1.0 C E:MET120 4.5 25.5 1.0 CG E:MET120 4.5 31.0 1.0 SD E:MET120 4.6 40.6 1.0 CA E:MET120 4.6 27.5 1.0 NZ E:LYS122 4.7 50.2 1.0 CG E:LYS122 4.8 41.0 1.0 CD E:LYS122 5.0 43.8 1.0

Chlorine binding site 4 out of 4 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.3. within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl301 b:40.7 occ:1.00 OG1 G:THR49 2.7 48.4 1.0 N H:SER91 3.3 25.6 1.0 CA G:GLY47 3.5 36.5 1.0 N G:THR49 3.5 29.8 1.0 CB H:THR90 3.6 31.4 1.0 N G:ALA50 3.6 23.6 1.0 CA H:THR90 3.7 34.9 1.0 C G:GLY47 3.7 35.2 1.0 N G:ALA48 3.8 32.1 1.0 CB G:THR49 3.9 33.1 1.0 OG H:SER91 3.9 32.9 1.0 C H:THR90 4.0 32.8 1.0 CA G:THR49 4.0 32.5 1.0 C G:THR49 4.1 30.8 1.0 CB H:SER91 4.1 31.0 1.0 CG2 H:THR90 4.3 26.3 1.0 CA H:SER91 4.3 28.5 1.0 CB G:ALA50 4.4 25.8 1.0 CA G:ALA50 4.4 28.7 1.0 O G:GLY47 4.4 35.0 1.0 OP2 I:DA111 4.6 54.0 1.0 C G:ALA48 4.6 35.7 1.0 N G:GLY47 4.6 35.9 1.0 CG2 G:THR49 4.6 42.9 1.0 OP1 I:DA111 4.7 50.4 1.0 OG1 H:THR90 4.7 34.6 1.0 CA G:ALA48 4.8 36.9 1.0

N.Horikoshi, Y.Arimura, H.Taguchi, H.Kurumizaka. Crystal Structures of Heterotypic Nucleosomes Containing Histones H2A.Z and H2A. Open Biology V. 6 2016.
ISSN: ESSN 2046-2441
PubMed: 27358293
DOI: 10.1098/RSOB.160127