Chlorine in PDB 3afa: The Human Nucleosome Structure

The structure of The Human Nucleosome Structure, PDB code: 3afa was solved by H.Tachiwana, W.Kagawa, A.Osakabe, K.Koichiro, T.Shiga, H.Kimura, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.839, 109.509, 180.919, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 27

The structure of The Human Nucleosome Structure also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

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

Chlorine binding site 1 out of 4 in the The Human Nucleosome Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Human Nucleosome Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:46.7 occ:1.00 N A:LYS122 3.2 33.6 1.0 CD A:PRO121 3.2 35.3 1.0 CB A:LYS122 3.3 34.3 1.0 CB A:MET120 3.6 31.7 1.0 N A:PRO121 3.7 34.9 1.0 CB A:PRO121 3.9 35.1 1.0 CA A:LYS122 3.9 33.0 1.0 CG A:PRO121 3.9 35.8 1.0 CE A:LYS122 4.1 39.7 1.0 C A:PRO121 4.2 35.0 1.0 CA A:PRO121 4.2 35.0 1.0 C A:MET120 4.3 34.0 1.0 CA A:MET120 4.5 31.0 1.0 CG A:LYS122 4.6 39.4 1.0 SD A:MET120 4.6 37.7 1.0 CD A:LYS122 4.6 41.1 1.0 CG A:MET120 4.7 34.2 1.0 NZ A:LYS122 4.8 42.2 1.0

Chlorine binding site 2 out of 4 in the The Human Nucleosome Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Human Nucleosome Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:40.4 occ:1.00 N C:GLY46 3.1 35.5 1.0 N D:SER91 3.2 33.9 1.0 CB D:THR90 3.5 32.5 1.0 CA C:GLY46 3.5 35.3 1.0 N C:ALA47 3.6 33.2 1.0 CA D:THR90 3.6 32.8 1.0 OP1 J:DT258 3.8 75.5 1.0 CA C:GLY44 3.8 40.1 1.0 C C:GLY44 3.8 38.9 1.0 N C:ALA45 3.9 38.3 1.0 C D:THR90 3.9 34.0 1.0 C C:GLY46 4.0 34.8 1.0 CB D:SER91 4.0 34.2 1.0 CG2 D:THR90 4.1 29.0 1.0 CA D:SER91 4.2 33.0 1.0 C C:ALA45 4.3 36.4 1.0 O C:GLY44 4.4 37.9 1.0 OG D:SER91 4.5 37.4 1.0 CA C:ALA45 4.6 37.7 1.0 CA C:ALA47 4.6 30.3 1.0 OG1 D:THR90 4.7 33.1 1.0 CB C:ALA47 4.8 35.1 1.0 N C:GLY44 4.9 41.6 1.0 N D:THR90 5.0 31.8 1.0

Chlorine binding site 3 out of 4 in the The Human Nucleosome Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Human Nucleosome Structure within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl201 b:40.4 occ:1.00 CB E:LYS122 3.3 31.7 1.0 N E:LYS122 3.3 29.2 1.0 CD E:PRO121 3.8 27.9 1.0 NZ E:LYS122 3.8 44.9 1.0 CA E:LYS122 3.8 29.7 1.0 CB E:MET120 3.9 29.9 1.0 N E:PRO121 4.0 29.1 1.0 CE E:LYS122 4.0 37.2 1.0 CG E:LYS122 4.0 35.9 1.0 CB E:PRO121 4.1 26.8 1.0 C E:PRO121 4.3 30.1 1.0 CA E:PRO121 4.4 28.8 1.0 CG E:PRO121 4.5 25.9 1.0 C E:MET120 4.5 28.1 1.0 SD E:MET120 4.6 39.6 1.0 CD E:LYS122 4.7 39.7 1.0 CA E:MET120 4.8 27.9 1.0 CG E:MET120 4.8 33.0 1.0

Chlorine binding site 4 out of 4 in the The Human Nucleosome Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Human Nucleosome Structure within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl201 b:38.2 occ:1.00 N G:GLY46 3.2 36.8 1.0 CA G:GLY44 3.4 41.0 1.0 N H:SER91 3.5 38.3 1.0 CB H:THR90 3.5 38.9 1.0 C G:GLY44 3.5 39.4 1.0 CA H:THR90 3.6 38.9 1.0 N G:ALA45 3.6 37.9 1.0 N G:ALA47 3.6 37.2 1.0 CA G:GLY46 3.7 36.6 1.0 C H:THR90 4.1 39.0 1.0 CG2 H:THR90 4.1 37.0 1.0 C G:GLY46 4.1 37.5 1.0 OG H:SER91 4.1 38.9 1.0 OP1 I:DA111 4.1 83.0 1.0 O G:GLY44 4.2 40.4 1.0 C G:ALA45 4.3 36.4 1.0 N G:GLY44 4.5 42.3 1.0 CB H:SER91 4.5 38.6 1.0 CA G:ALA45 4.5 37.7 1.0 CA H:SER91 4.6 38.3 1.0 CA G:ALA47 4.7 34.7 1.0 CB G:ALA47 4.7 36.6 1.0 OG1 H:THR90 4.7 38.0 1.0 N H:THR90 4.9 38.2 1.0 O H:ILE89 4.9 36.6 1.0

H.Tachiwana, W.Kagawa, A.Osakabe, K.Kawaguchi, T.Shiga, Y.Hayashi-Takanaka, H.Kimura, H.Kurumizaka. Structural Basis of Instability of the Nucleosome Containing A Testis-Specific Histone Variant, Human H3T Proc.Natl.Acad.Sci.Usa V. 107 10454 2010.
ISSN: ISSN 0027-8424
PubMed: 20498094
DOI: 10.1073/PNAS.1003064107