Chlorine in PDB 5b31: The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.

The structure of The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1., PDB code: 5b31 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)	48.62 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.110, 109.685, 181.487, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 27.1

The structure of The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1. also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Chlorine atom in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1. (pdb code 5b31). 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 H3.1., PDB code: 5b31:
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 H3.1.


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 H3.1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:54.5 occ:1.00 N A:LYS122 3.1 32.4 1.0 CD A:PRO121 3.3 39.2 1.0 N A:PRO121 3.6 40.0 1.0 CB A:LYS122 3.6 30.4 1.0 CG A:LYS122 3.6 33.0 1.0 CE A:LYS122 3.8 47.4 1.0 CB A:PRO121 3.8 37.6 1.0 CB A:MET120 3.9 36.3 1.0 CG A:PRO121 3.9 39.0 1.0 CA A:LYS122 3.9 33.8 1.0 C A:PRO121 4.0 38.2 1.0 CA A:PRO121 4.0 36.9 1.0 C A:MET120 4.3 36.7 1.0 CD A:LYS122 4.3 38.0 1.0 CA A:MET120 4.6 36.8 1.0 SD A:MET120 4.8 51.4 1.0 CG A:MET120 4.9 37.8 1.0

Chlorine binding site 2 out of 4 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.


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 H3.1. within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:50.1 occ:1.00 N C:GLY46 3.1 36.2 1.0 N D:SER91 3.2 34.5 1.0 CB D:THR90 3.4 37.9 1.0 CA C:GLY46 3.5 27.4 1.0 CA D:THR90 3.7 36.6 1.0 N C:ALA47 3.7 34.8 1.0 CA C:GLY44 3.7 40.9 1.0 C C:GLY44 3.8 41.4 1.0 N C:ALA45 3.8 47.9 1.0 OP1 J:DT258 3.9 55.3 1.0 C D:THR90 3.9 39.7 1.0 C C:GLY46 3.9 38.0 1.0 CG2 D:THR90 4.1 37.8 1.0 OG D:SER91 4.1 38.9 1.0 CB D:SER91 4.2 33.5 1.0 C C:ALA45 4.3 36.1 1.0 CA D:SER91 4.3 33.9 1.0 O C:GLY44 4.3 40.2 1.0 OG1 D:THR90 4.5 34.7 1.0 CA C:ALA45 4.6 39.2 1.0 CA C:ALA47 4.7 33.8 1.0 N C:GLY44 4.8 39.0 1.0 CB C:ALA47 5.0 31.0 1.0

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


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 H3.1. within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl302 b:49.6 occ:1.00 N E:LYS122 3.1 25.4 1.0 CD E:PRO121 3.5 33.8 1.0 CB E:LYS122 3.6 30.8 1.0 CB E:PRO121 3.7 30.9 1.0 CG E:LYS122 3.7 33.1 1.0 N E:PRO121 3.7 30.5 1.0 CB E:MET120 3.8 32.1 1.0 CA E:LYS122 3.9 31.2 1.0 C E:PRO121 4.0 31.8 1.0 CA E:PRO121 4.0 26.9 1.0 CG E:PRO121 4.1 30.9 1.0 CD E:LYS122 4.1 37.7 1.0 C E:MET120 4.3 31.9 1.0 CE E:LYS122 4.5 37.0 1.0 CA E:MET120 4.6 31.5 1.0 CG E:MET120 4.7 34.0 1.0 SD E:MET120 4.9 42.0 1.0

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


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 H3.1. within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl301 b:49.5 occ:1.00 OG1 G:THR49 3.0 51.9 1.0 N H:SER91 3.3 35.7 1.0 CA G:GLY47 3.4 42.5 1.0 N G:THR49 3.4 39.6 1.0 N G:ALA50 3.5 40.5 1.0 C G:GLY47 3.5 48.0 1.0 OG H:SER91 3.6 42.5 1.0 CB H:THR90 3.7 37.5 1.0 CA H:THR90 3.7 38.0 1.0 N G:ALA48 3.8 47.5 1.0 CB H:SER91 4.0 36.0 1.0 C H:THR90 4.0 40.2 1.0 CA G:THR49 4.0 42.5 1.0 CB G:THR49 4.0 45.5 1.0 C G:THR49 4.1 43.2 1.0 O G:GLY47 4.1 45.8 1.0 CA H:SER91 4.2 37.1 1.0 CB G:ALA50 4.3 36.6 1.0 CG2 H:THR90 4.3 43.4 1.0 N G:GLY47 4.3 46.0 1.0 CA G:ALA50 4.3 41.1 1.0 C G:ALA48 4.5 41.7 1.0 CG2 G:THR49 4.6 45.8 1.0 CA G:ALA48 4.6 46.2 1.0 OP1 I:DA111 4.7 62.5 1.0 OG1 H:THR90 4.8 42.4 1.0 O H:ILE89 4.9 43.2 1.0 N H:THR90 5.0 38.8 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